bims-pideca 2020-08-09 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2020–08–09
eleven papers selected by
Ralitsa Radostinova Madsen, University College London

Selective inhibition of mTORC1 in tumor vessels increases antitumor immunity.
Inhibition of the PI 3-kinase pathway disrupts the unfolded protein response and reduces sensitivity to ER stress-dependent apoptosis.
Metabolic stress regulates genome-wide transcription in a PTEN-dependent manner.
Increased PIP3 activity blocks nanoparticle mRNA delivery.
The Structural Determinants of PH Domain-Mediated Regulation of Akt Revealed by Segmental Labeling.
A Xenograft Model for Venous Malformation.
An information theoretic approach to insulin sensing by human kidney podocytes.
Stromal Cell-Contact Dependent PI3K and APRIL Induced NF-κB Signaling Prevent Mitochondrial- and ER Stress Induced Death of Memory Plasma Cells.
Patterns of Ciliation and Ciliary Signaling in Cancer.
Dynamic changes in the epigenomic landscape regulate human organogenesis and link to developmental disorders.
PIP2: A critical regulator of vascular ion channels hiding in plain sight.

JCI Insight. 2020 Aug 06. pii: 139237. [Epub ahead of print]5(15):

Selective inhibition of mTORC1 in tumor vessels increases antitumor immunity.

Shan Wang, Ariel Raybuck, Eileen Shiuan, Sung Hoon Cho, Qingfei Wang, Dana M Brantley-Sieders, Deanna Edwards, Margaret M Allaman, James Nathan, Keith T Wilson, David DeNardo, Siyuan Zhang, Rebecca Cook, Mark Boothby, Jin Chen.

  A tumor blood vessel is a key regulator of tissue perfusion, immune cell trafficking, cancer metastasis, and therapeutic responsiveness. mTORC1 is a signaling node downstream of multiple angiogenic factors in the endothelium. However, mTORC1 inhibitors have limited efficacy in most solid tumors, in part due to inhibition of immune function at high doses used in oncology patients and compensatory PI3K signaling triggered by mTORC1 inhibition in tumor cells. Here we show that low-dose RAD001/everolimus, an mTORC1 inhibitor, selectively targets mTORC1 signaling in endothelial cells (ECs) without affecting tumor cells or immune cells, resulting in tumor vessel normalization and increased antitumor immunity. Notably, this phenotype was recapitulated upon targeted inducible gene ablation of the mTORC1 component Raptor in tumor ECs (RaptorECKO). Tumors grown in RaptorECKO mice displayed a robust increase in tumor-infiltrating lymphocytes due to GM-CSF-mediated activation of CD103+ dendritic cells and displayed decreased tumor growth and metastasis. GM-CSF neutralization restored tumor growth and metastasis, as did T cell depletion. Importantly, analyses of human tumor data sets support our animal studies. Collectively, these findings demonstrate that endothelial mTORC1 is an actionable target for tumor vessel normalization, which could be leveraged to enhance antitumor immune therapies.

Keywords:  Cancer immunotherapy; Immunology; Oncology; endothelial cells

DOI:  https://doi.org/10.1172/jci.insight.139237
FASEB J. 2020 Aug 03.

Inhibition of the PI 3-kinase pathway disrupts the unfolded protein response and reduces sensitivity to ER stress-dependent apoptosis.

Jonathon N Winnay, Marie H Solheim, Masaji Sakaguchi, Pål R Njølstad, C Ronald Kahn.

  Class Ia phosphoinositide 3-kinases (PI3K) are critical mediators of insulin and growth factor action. We have demonstrated that the p85α regulatory subunit of PI3K modulates the unfolded protein response (UPR) by interacting with and regulating the nuclear translocation of XBP-1s, a transcription factor essential for the UPR. We now show that PI3K activity is required for full activation of the UPR. Pharmacological inhibition of PI3K in cells blunts the ER stress-dependent phosphorylation of IRE1α and PERK, decreases induction of ATF4, CHOP, and XBP-1 and upregulates UPR target genes. Cells expressing a human p85α mutant (R649W) previously shown to inhibit PI3K, exhibit decreased activation of IRE1α and PERK and reduced induction of CHOP and ATF4. Pharmacological inhibition of PI3K, overexpression of a mutant of p85α that lacks the ability to interact with the p110α catalytic subunit (∆p85α) or expression of mutant p85α (R649W) in vivo, decreased UPR-dependent induction of ER stress response genes. Acute tunicamycin treatment of R649W+/- mice revealed reduced induction of UPR target genes in adipose tissue, whereas chronic tunicamycin exposure caused sustained increases in UPR target genes in adipose tissue. Finally, R649W+/- cells exhibited a dramatic resistance to ER stress-dependent apoptosis. These data suggest that PI3K pathway dysfunction causes ER stress that may drive the pathogenesis of several diseases including Type 2 diabetes and various cancers.

Keywords:  Apoptosis; ER stress; PI 3-kinase; SHORT Syndrome; Unfolded Protein Response

DOI:  https://doi.org/10.1096/fj.202000892R
Hum Mol Genet. 2020 Aug 03. pii: ddaa168. [Epub ahead of print]

Metabolic stress regulates genome-wide transcription in a PTEN-dependent manner.

Ata Abbas, Roshan Padmanabhan, Charis Eng.

PTEN is implicated in a wide variety of pathophysiological conditions and traditionally studied in the context of the PIK3-AKT-mTOR axis. Recent studies from our group and others have reported a novel role of PTEN in the regulation of transcription at the genome-wide scale. This emerging role of PTEN on global transcriptional regulation is providing a better understanding of various diseases, including cancer. Since cancer progression is an energy-demanding process and PTEN is known to regulate metabolic processes, we sought to understand the role of PTEN in transcriptional regulation under metabolic stress, a condition often developing in the tumor microenvironment. In the present study, we demonstrate that PTEN modulates genome-wide RNA Polymerase II (Pol II) occupancy in cells undergoing glucose deprivation. The glucose-deprived PTEN null cells were found to continue global gene transcription, which may activate a survival mode. However, cells with constitutive PTEN expression slow transcription, an evolutionary mechanism that may save cellular energy and activate programmed cell death pathways, in the absence of glucose. Interestingly, alternative exon usage by PTEN null cells is increased under metabolic stress compared to PTEN expressing cells. Overall, our study demonstrates distinct mechanisms involved in PTEN-dependent genome-wide transcriptional control under metabolic stress. Our findings provide a new insight in understanding tumor pathology and how PTEN loss of function, whether by genetic or non-genetic mechanisms, can contribute to a favorable transcriptional program employed by tumor cells to escape apoptosis, hence developing more aggressive and metastatic phenotypes.

DOI: https://doi.org/10.1093/hmg/ddaa168
Sci Adv. 2020 Jul;6(30): eaba5672

Increased PIP3 activity blocks nanoparticle mRNA delivery.

Kalina Paunovska, Alejandro Da Silva Sanchez, Matthew T Foster, David Loughrey, Emmeline L Blanchard, Fatima Z Islam, Zubao Gan, Athanasios Mantalaris, Philip J Santangelo, James E Dahlman.

The biological pathways that affect drug delivery in vivo remain poorly understood. We hypothesized that altering cell metabolism with phosphatidylinositol (3,4,5)-triphosphate (PIP3), a bioactive lipid upstream of the metabolic pathway PI3K (phosphatidylinositol 3-kinase)/AKT/ mTOR (mammalian target of rapamycin) would transiently increase protein translated by nanoparticle-delivered messenger RNA (mRNA) since these pathways increase growth and proliferation. Instead, we found that PIP3 blocked delivery of clinically-relevant lipid nanoparticles (LNPs) across multiple cell types in vitro and in vivo. PIP3-driven reductions in LNP delivery were not caused by toxicity, cell uptake, or endosomal escape. Interestingly, RNA sequencing and metabolomics analyses suggested an increase in basal metabolic rate. Higher transcriptional activity and mitochondrial expansion led us to formulate two competing hypotheses that explain the reductions in LNP-mediated mRNA delivery. First, PIP3 induced consumption of limited cellular resources, "drowning out" exogenously-delivered mRNA. Second, PIP3 triggers a catabolic response that leads to protein degradation and decreased translation.

DOI: https://doi.org/10.1126/sciadv.aba5672
Elife. 2020 Aug 03. pii: e59151. [Epub ahead of print]9

The Structural Determinants of PH Domain-Mediated Regulation of Akt Revealed by Segmental Labeling.

Nam Chu, Thibault Viennet, Hwan Bae, Antonieta Salguero, Andras Boeszoermenyi, Haribabu Arthanari, Philip A Cole.

  Akt is a critical protein kinase that governs cancer cell growth and metabolism. Akt appears to be autoinhibited by an intramolecular interaction between its N-terminal pleckstrin homology (PH) domain and kinase domain, which is relieved by C-tail phosphorylation, but the precise molecular mechanisms remain elusive. Here we use a combination of protein semisynthesis, NMR, and enzymological analysis to characterize structural features of the PH domain in its autoinhibited and activated states. We find that Akt autoinhibition depends on the length/flexibility of the PH-kinase linker. We identify a role for a dynamic short segment in the PH domain that appears to regulate autoinhibition and PDK1-catalyzed phosphorylation of Thr308 in the activation loop. We determine that Akt allosteric inhibitor MK2206 drives distinct PH domain structural changes compared to baseline autoinhibited Akt. These results highlight how the conformational plasticity of Akt governs the delicate control of its catalytic properties.

Keywords:  biochemistry; chemical biology; human

DOI:  https://doi.org/10.7554/eLife.59151
Methods Mol Biol. 2021 ;2206 179-192

A Xenograft Model for Venous Malformation.

Jillian Goines, Elisa Boscolo.

  Xenograft models allow for an in vivo approach to monitor cellular functions within the context of a host microenvironment. Here we describe a protocol to generate a xenograft model of venous malformation (VM) based on the use of human umbilical vein endothelial cells (HUVEC) expressing a constitutive active form of the endothelial tyrosine kinase receptor TEK (TIE2 p.L914F) or patient-derived EC containing TIE2 and/or PIK3CA gene mutations. Hyperactive somatic TIE2 and PIK3CA mutations are a common hallmark of VM in patient lesions. The EC are injected subcutaneously on the back of athymic nude mice to generate ectatic vascular channels and recapitulate histopathological features of VM patient tissue histology. Lesion plugs with TIE2/PIK3CA-mutant EC are visibly vascularized within 7-9 days of subcutaneous injection, making this a great tool to study venous malformation.

Keywords:  Endothelial cells; TIE2; Venous malformation; Xenograft model

DOI:  https://doi.org/10.1007/978-1-0716-0916-3_13
Mol Cell Endocrinol. 2020 Aug 01. pii: S0303-7207(20)30276-8. [Epub ahead of print] 110976

An information theoretic approach to insulin sensing by human kidney podocytes.

Robert Jp Pope, Kathryn L Garner, Margaritis Voliotis, Abigail C Lay, Virginie Ms Betin, Krasimira Tsaneva-Atanasova, Gavin I Welsh, Richard Jm Coward, Craig A McArdle.

  Podocytes are key components of the glomerular filtration barrier (GFB). They are insulin-responsive but can become insulin-resistant, causing features of the leading global cause of kidney failure, diabetic nephropathy. Insulin acts via insulin receptors to control activities fundamental to GFB integrity, but the amount of information transferred is unknown. Here we measure this in human podocytes, using information theory-derived statistics that take into account cell-cell variability. High content imaging was used to measure insulin effects on Akt, FOXO and ERK. Mutual Information (MI) and Channel Capacity (CC) were calculated as measures of information transfer. We find that insulin acts via noisy communication channels with more information flow to Akt than to ERK. Information flow estimates were increased by consideration of joint sensing (ERK and Akt) and response trajectory (live cell imaging of FOXO1-clover translocation). Nevertheless, MI values were always <1Bit as most information was lost through signaling. Constitutive PI3K activity is a predominant feature of the system that restricts the proportion of CC engaged by insulin. Negative feedback from Akt supressed this activity and thereby improved insulin sensing, whereas sensing was robust to manipulation of feedforward signaling by inhibiting PI3K, PTEN or PTP1B. The decisions made by individual podocytes dictate GFB integrity, so we suggest that understanding the information on which the decisions are based will improve understanding of diabetic kidney disease and its treatment.

Keywords:  Cell signaling; Diabetes; Insulin receptor; Mutual information; Phosphatidyl-inositol 3 kinase (PI3K); Podocyte

DOI:  https://doi.org/10.1016/j.mce.2020.110976
Cell Rep. 2020 Aug 04. pii: S2211-1247(20)30967-0. [Epub ahead of print]32(5): 107982

Stromal Cell-Contact Dependent PI3K and APRIL Induced NF-κB Signaling Prevent Mitochondrial- and ER Stress Induced Death of Memory Plasma Cells.

Rebecca Cornelis, Stefanie Hahne, Adriano Taddeo, Georg Petkau, Darya Malko, Pawel Durek, Manja Thiem, Lukas Heiberger, Lena Peter, Elodie Mohr, Cora Klaeden, Koji Tokoyoda, Francesco Siracusa, Bimba Franziska Hoyer, Falk Hiepe, Mir-Farzin Mashreghi, Fritz Melchers, Hyun-Dong Chang, Andreas Radbruch.

  The persistence of long-lived memory plasma cells in the bone marrow depends on survival factors available in the bone marrow, which are provided in niches organized by stromal cells. Using an ex vivo system in which we supply the known survival signals, direct cell contact to stromal cells, and the soluble cytokine a proliferation-inducing ligand (APRIL), we have elucidated the critical signaling pathways required for the survival of long-lived plasma cells. Integrin-mediated contact of bone marrow plasma cells with stromal cells activates the phosphatidylinositol 3-kinase (PI3K) signaling pathway, leading to critical inactivation of Forkhead-Box-Protein O1/3 (FoxO1/3) and preventing the activation of mitochondrial stress-associated effector caspases 3 and 7. Accordingly, inhibition of PI3K signaling in vivo ablates bone marrow plasma cells. APRIL signaling, by the nuclear factor κB (NF-κB) pathway, blocks activation of the endoplasmic-reticulum-stress-associated initiator caspase 12. Thus, stromal-cell-contact-induced PI3K and APRIL-induced NF-κB signaling provide the necessary and complementary signals to maintain bone marrow memory plasma cells.

Keywords:  APRIL; BCMA; FoxO; IRF4; PI3K/AKT; bone marrow; caspase 12; caspase 3; caspase 7; long-lived memory PCs; stromal cell

DOI:  https://doi.org/10.1016/j.celrep.2020.107982
Rev Physiol Biochem Pharmacol. 2020 Aug 07.

Patterns of Ciliation and Ciliary Signaling in Cancer.

Anna A Kiseleva, Anna S Nikonova, Erica A Golemis.

  Among the factors that have been strongly implicated in regulating cancerous transformation, the primary monocilium (cilium) has gained increasing attention. The cilium is a small organelle extending from the plasma membrane, which provides a localized hub for concentration of transmembrane receptors. These receptors transmit signals from soluble factors (including Sonic hedgehog (SHH), platelet-derived growth factor (PDGF-AA), WNT, TGFβ, NOTCH, and others) that regulate cell growth, as well as mechanosensory cues provided by flow or extracellular matrix. Ciliation is regulated by cell cycle, with most cells that are in G0 (quiescent) or early G1 ciliation and cilia typically absent in G2/M cells. Notably, while most cells organized in solid tissues are ciliated, cancerous transformation induces significant changes in ciliation. Most cancer cells lose cilia; medulloblastomas and basal cell carcinomas, dependent on an active SHH pathway, rely on ciliary maintenance. Changes in cancer cell ciliation are driven by core oncogenic pathways (EGFR, KRAS, AURKA, PI3K), and importantly ciliation status regulates functionality of those pathways. Ciliation is both influenced by targeted cancer therapies and linked to therapeutic resistance; recent studies suggest ciliation may also influence cancer cell metabolism and stem cell identity. We review recent studies defining the relationship between cilia and cancer.

Keywords:  Aurora-A; Cilium; Extracellular vesicle; NEDD9; Stroma; Targeted therapy

DOI:  https://doi.org/10.1007/112_2020_36
Nat Commun. 2020 Aug 06. 11(1): 3920

Dynamic changes in the epigenomic landscape regulate human organogenesis and link to developmental disorders.

Dave T Gerrard, Andrew A Berry, Rachel E Jennings, Matthew J Birket, Peyman Zarrineh, Myles G Garstang, Sarah L Withey, Patrick Short, Sandra Jiménez-Gancedo, Panos N Firbas, Ian Donaldson, Andrew D Sharrocks, Karen Piper Hanley, Matthew E Hurles, José Luis Gomez-Skarmeta, Nicoletta Bobola, Neil A Hanley.

How the genome activates or silences transcriptional programmes governs organ formation. Little is known in human embryos undermining our ability to benchmark the fidelity of stem cell differentiation or cell programming, or interpret the pathogenicity of noncoding variation. Here, we study histone modifications across thirteen tissues during human organogenesis. We integrate the data with transcription to build an overview of how the human genome differentially regulates alternative organ fates including by repression. Promoters from nearly 20,000 genes partition into discrete states. Key developmental gene sets are actively repressed outside of the appropriate organ without obvious bivalency. Candidate enhancers, functional in zebrafish, allow imputation of tissue-specific and shared patterns of transcription factor binding. Overlaying more than 700 noncoding mutations from patients with developmental disorders allows correlation to unanticipated target genes. Taken together, the data provide a comprehensive genomic framework for investigating normal and abnormal human development.

DOI: https://doi.org/10.1038/s41467-020-17305-2
Proc Natl Acad Sci U S A. 2020 Aug 06. pii: 202006737. [Epub ahead of print]

PIP2: A critical regulator of vascular ion channels hiding in plain sight.

Osama F Harraz, David Hill-Eubanks, Mark T Nelson.

  The phosphoinositide, phosphatidylinositol 4,5-bisphosphate (PIP2), has long been established as a major contributor to intracellular signaling, primarily by virtue of its role as a substrate for phospholipase C (PLC). Signaling by Gq-protein-coupled receptors triggers PLC-mediated hydrolysis of PIP2 into inositol 1,4,5-trisphosphate and diacylglycerol, which are well known to modulate vascular ion channel activity. Often overlooked, however, is the role PIP2 itself plays in this regulation. Although numerous reports have demonstrated that PIP2 is critical for ion channel regulation, how it impacts vascular function has received scant attention. In this review, we focus on PIP2 as a regulator of ion channels in smooth muscle cells and endothelial cells-the two major classes of vascular cells. We further address the concerted effects of such regulation on vascular function and blood flow control. We close with a consideration of current knowledge regarding disruption of PIP2 regulation of vascular ion channels in disease.

Keywords:  GPCR; PIP2; endothelial cell; ion channel; smooth muscle cell

DOI:  https://doi.org/10.1073/pnas.2006737117