bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023–01–22
twelve papers selected by
Ralitsa Radostinova Madsen, University College London
  1. NFκB-Mediated Expression of Phosphoinositide 3-Kinase δ Is Critical for Mesenchymal Transition in Retinal Pigment Epithelial Cells.
  2. Response to sirolimus in capillary lymphatic venous malformations and associated syndromes: Impact on symptomatology, quality of life, and radiographic response.
  3. Recent advances in kinase signaling network profiling by mass spectrometry.
  4. HER2-driven breast cancer suppression by the JNK signaling pathway.
  5. Acetyl-CoA metabolism in cancer.
  6. INPP4A-related genetic and phenotypic spectrum and functional relevance of subcellular targeting of INPP4A isoforms.
  7. Protein kinase B (PKB/AKT) protects IDH-mutated glioma from ferroptosis via Nrf2.
  8. Quantifying stimulus-response specificity to probe the functional state of macrophages.
  9. Cell survival following direct executioner-caspase activation.
  10. Phosphosite Scanning reveals a complex phosphorylation code underlying CDK-dependent activation of Hcm1.
  11. Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition.
  12. Hepatic nonvesicular cholesterol transport is critical for systemic lipid homeostasis.
  1. Cells. 2023 Jan 04. pii: 207. [Epub ahead of print]12(2):
    NFκB-Mediated Expression of Phosphoinositide 3-Kinase δ Is Critical for Mesenchymal Transition in Retinal Pigment Epithelial Cells.
    Haote Han, Yanhui Yang, Zhuo Han, Luping Wang, Lijun Dong, Hui Qi, Bing Liu, Jingkui Tian, Bart Vanhaesebroeck, Andrius Kazlauskas, Guoming Zhang, Shaochong Zhang, Hetian Lei.
      Epithelial mesenchymal transition (EMT) plays a vital role in a variety of human diseases including proliferative vitreoretinopathy (PVR), in which retinal pigment epithelial (RPE) cells play a key part. Transcriptomic analysis showed that the phosphoinositide 3-kinase (PI3K)/Akt signaling pathway was up-regulated in human RPE cells upon treatment with transforming growth factor (TGF)-β2, a multifunctional cytokine associated with clinical PVR. Stimulation of human RPE cells with TGF-β2 induced expression of p110δ (the catalytic subunit of PI3Kδ) and activation of NFκB/p65. CRISPR-Cas9-mediated depletion of p110δ or NFκB/p65 suppressed TGF-β2-induced fibronectin expression and activation of Akt as well as migration of these cells. Intriguingly, abrogating expression of NFκB/p65 also blocked TGF-β2-induced expression of p110δ, and luciferase reporter assay indicated that TGF-β2 induced NFκB/p65 binding to the promoter of the PIK3CD that encodes p110δ. These data reveal that NFκB/p65-mediated expression of PI3Kδ is essential in human RPE cells for TGF-β2-induced EMT, uncovering hindrance of TGF-β2-induced expression of p110δ as a novel approach to inhibit PVR.
    Keywords:  CRISPR/Cas9; EMT; NFκB/p65; PI3Kδ; PVR; RPE; TGF-β2
    DOI:  https://doi.org/10.3390/cells12020207
  2. Pediatr Blood Cancer. 2023 Jan 18. e30215
    Response to sirolimus in capillary lymphatic venous malformations and associated syndromes: Impact on symptomatology, quality of life, and radiographic response.
    Elissa R Engel, Adrienne Hammill, Denise Adams, Roderic J Phillips, Michael Jeng, Megha M Tollefson, Ionela Iacobas, Deborah Schiff, Shoshana Greenberger, Michael Kelly, Ilona Frieden, Nibal Zaghloul, Beth Drolet, Amy Geddis, Dov Goldenberg, Kiersten Ricci.
       BACKGROUND: Capillary lymphatic venous malformations (CLVM) and associated syndromes, including Klippel-Trenaunay syndrome (KTS) and congenital lipomatous overgrowth, vascular malformation, epidermal nevi, skeletal, and spinal syndrome (CLOVES), are underrecognized disorders associated with high morbidity from chronic pain, recurrent infections, bleeding, and clotting complications. The rarity of these disorders and heterogeneity of clinical presentations make large-scale randomized clinical drug trials challenging. Identification of PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha [gene]) mutations in CLVM has made targeted medications, such as sirolimus, attractive treatment options. The aim of this study was to investigate the safety and efficacy of sirolimus therapy in CLVM.
    PROCEDURE: A combined prospective and retrospective cohort of pediatric and young adult patients with CLVM treated with sirolimus was evaluated for disease response, including symptom improvement, quality of life (QOL), and radiologic response. Sirolimus dosing regimens and toxicities were also assessed.
    RESULTS: Twenty-nine patients with CLVM, including KTS and CLOVES, were included. Ninety-three percent of patients reported improved QOL, and 86% had improvement in at least one symptom. Most significantly, improvement was noted in 100% of patients with bleeding and 89% with thrombotic complications with corresponding decreases in mean D-dimer (p = .008) and increases in mean fibrinogen (p = .016). No patients had progressive disease on sirolimus. Most common side effects included neutropenia, lymphopenia, infection, and aphthous ulcers/stomatitis. No toxicities were life-threatening, and none required long-term discontinuation of sirolimus.
    CONCLUSION: Sirolimus appears to be effective at reducing complications and improving QOL in patients with CLVM and associated syndromes. In this patient cohort, sirolimus was well tolerated and resulted in few treatment-related toxicities.
    Keywords:  CLOVES; Klippel-Trenaunay syndrome (KTS); PIK3CA-related overgrowth spectrum (PROS); capillary lymphatic venous malformation (CLVM); mammalian target of rapamycin (mTOR); sirolimus (rapamycin)
    DOI:  https://doi.org/10.1002/pbc.30215
  3. Curr Opin Chem Biol. 2023 Jan 17. pii: S1367-5931(22)00145-4. [Epub ahead of print]73 102260
    Recent advances in kinase signaling network profiling by mass spectrometry.
    Giulia Franciosa, Marie Locard-Paulet, Lars J Jensen, Jesper V Olsen.
      Mass spectrometry-based phosphoproteomics is currently the leading methodology for the study of global kinase signaling. The scientific community is continuously releasing technological improvements for sensitive and fast identification of phosphopeptides, and their accurate quantification. To interpret large-scale phosphoproteomics data, numerous bioinformatic resources are available that help understanding kinase network functional role in biological systems upon perturbation. Some of these resources are databases of phosphorylation sites, protein kinases and phosphatases; others are bioinformatic algorithms to infer kinase activity, predict phosphosite functional relevance and visualize kinase signaling networks. In this review, we present the latest experimental and bioinformatic tools to profile protein kinase signaling networks and provide examples of their application in biomedicine.
    Keywords:  Kinase; Phosphoproteomics; Phosphorylation; Signaling
    DOI:  https://doi.org/10.1016/j.cbpa.2022.102260
  4. Proc Natl Acad Sci U S A. 2023 Jan 24. 120(4): e2218373120
    HER2-driven breast cancer suppression by the JNK signaling pathway.
    Zeynep Itah, Shanzah Chaudhry, Sithara Raju Ponny, Ozkan Aydemir, Alexandra Lee, Julie Cavanagh-Kyros, Cathy Tournier, William J Muller, Roger J Davis.
      The HER2+ subtype of human breast cancer is associated with the malignant transformation of luminal ductal cells of the mammary epithelium. The sequence analysis of tumor DNA identifies loss of function mutations and deletions of the MAP2K4 and MAP2K7 genes that encode direct activators of the JUN NH2-terminal kinase (JNK). We report that in vitro studies of human mammary epithelial cells with CRISPR-induced mutations in the MAPK and MAP2K components of the JNK pathway caused no change in growth in 2D culture, but these mutations promoted epithelial cell proliferation in 3D culture. Analysis of gene expression signatures in 3D culture demonstrated similar changes caused by HER2 activation and JNK pathway loss. The mechanism of signal transduction cross-talk may be mediated, in part, by JNK-suppressed expression of integrin α6β4 that binds HER2 and amplifies HER2 signaling. These data suggest that HER2 activation and JNK pathway loss may synergize to promote breast cancer. To test this hypothesis, we performed in vivo studies using a mouse model of HER2+ breast cancer with Cre/loxP-mediated ablation of genes encoding JNK (Mapk8 and Mapk9) and the MAP2K (Map2k4 and Map2k7) that activate JNK in mammary epithelial cells. Kaplan-Meier analysis of tumor development demonstrated that JNK pathway deficiency promotes HER2+-driven breast cancer. Collectively, these data identify JNK pathway genes as potential suppressors for HER2+ breast cancer.
    Keywords:  HER2+ breast cancer; JNK; MAP2K4; MAP2K7; integrin α6β4
    DOI:  https://doi.org/10.1073/pnas.2218373120
  5. Nat Rev Cancer. 2023 Jan 19.
    Acetyl-CoA metabolism in cancer.
    David A Guertin, Kathryn E Wellen.
      Few metabolites can claim a more central and versatile role in cell metabolism than acetyl coenzyme A (acetyl-CoA). Acetyl-CoA is produced during nutrient catabolism to fuel the tricarboxylic acid cycle and is the essential building block for fatty acid and isoprenoid biosynthesis. It also functions as a signalling metabolite as the substrate for lysine acetylation reactions, enabling the modulation of protein functions in response to acetyl-CoA availability. Recent years have seen exciting advances in our understanding of acetyl-CoA metabolism in normal physiology and in cancer, buoyed by new mouse models, in vivo stable-isotope tracing approaches and improved methods for measuring acetyl-CoA, including in specific subcellular compartments. Efforts to target acetyl-CoA metabolic enzymes are also advancing, with one therapeutic agent targeting acetyl-CoA synthesis receiving approval from the US Food and Drug Administration. In this Review, we give an overview of the regulation and cancer relevance of major metabolic pathways in which acetyl-CoA participates. We further discuss recent advances in understanding acetyl-CoA metabolism in normal tissues and tumours and the potential for targeting these pathways therapeutically. We conclude with a commentary on emerging nodes of acetyl-CoA metabolism that may impact cancer biology.
    DOI:  https://doi.org/10.1038/s41568-022-00543-5
  6. Neurogenetics. 2023 Jan 19.
    INPP4A-related genetic and phenotypic spectrum and functional relevance of subcellular targeting of INPP4A isoforms.
    Laura Hecher, Frederike L Harms, Jasmin Lisfeld, Malik Alawi, Jonas Denecke, Kerstin Kutsche.
      Type I inositol polyphosphate-4-phosphatase (INPP4A) belongs to the group of phosphoinositide phosphatases controlling proliferation, apoptosis, and endosome function by hydrolyzing phosphatidylinositol 3,4-bisphosphate. INPP4A produces multiple transcripts encoding shorter and longer INPP4A isoforms with hydrophilic or hydrophobic C-terminus. Biallelic INPP4A truncating variants cause a spectrum of neurodevelopmental disorders ranging from moderate intellectual disability to postnatal microcephaly with developmental and epileptic encephalopathy and (ponto)cerebellar hypoplasia. We report a girl with the novel homozygous INPP4A variant NM_001134224.2:c.2840del/p.(Gly947Glufs*12) (isoform d). She presented with postnatal microcephaly, global developmental delay, visual impairment, myoclonic seizures, and pontocerebellar hypoplasia and died at the age of 27 months. The level of mutant INPP4A mRNAs in proband-derived leukocytes was comparable to controls suggesting production of C-terminally altered INPP4A isoforms. We transiently expressed eGFP-tagged INPP4A isoform a (NM_004027.3) wildtype and p.(Gly908Glufs*12) mutant [p.(Gly947Glufs*12) according to NM_001134224.2] as well as INPP4A isoform b (NM_001566.2) wildtype and p.(Asp915Alafs*2) mutant, previously reported in family members with moderate intellectual disability, in HeLa cells and determined their subcellular distributions. While INPP4A isoform a was preferentially found in perinuclear clusters co-localizing with the GTPase Rab5, isoform b showed a net-like distribution, possibly localizing near and/or on microtubules. Quantification of intracellular localization patterns of the two INPP4A mutants revealed significant differences compared with the respective wildtype and similarity with each other. Our data suggests an important non-redundant function of INPP4A isoforms with hydrophobic or hydrophilic C-terminus in the brain.
    Keywords:  Alternative splicing; Endocytosis; Phosphatidylinositol 3-phosphate; Pontocerebellar hypoplasia; Vesicular traffic
    DOI:  https://doi.org/10.1007/s10048-023-00709-9
  7. Clin Cancer Res. 2023 Jan 17. pii: CCR-22-3179. [Epub ahead of print]
    Protein kinase B (PKB/AKT) protects IDH-mutated glioma from ferroptosis via Nrf2.
    Yang Liu, Fu-Ju Chou, Fengchao Lang, Meili Zhang, Hua Song, Wei Zhang, Dionne L Davis, Nicole J Briceno, Yang Zhang, Patrick J Cimino, Kareem A Zaghloul, Mark R Gilbert, Terri S Armstrong, Chunzhang Yang.
       PURPOSE: Mutations of the isocitrate dehydrogenase (IDH) gene are common genetic mutations in human malignancies. Increasing evidence indicates that IDH mutations play critical roles in malignant transformation and progression. However, the therapeutic options for IDH-mutated cancers remain limited. In this study, the investigation of patient cohorts revealed that the phosphatidylinositol-3 kinase (PI3Ks)/protein kinase B (AKT) signaling pathways were enhanced in IDH-mutated cancer cells.
    EXPERIMENTAL DESIGN: In this study, we investigated the gene expression profile in IDH-mutated cells using RNA sequencing after the depletion of AKT. Gene set enrichment analysis (GSEA) and pathway enrichment analysis were used to discover altered molecular pathways due to AKT depletion. We further investigated the therapeutic effect of the AKT inhibitor, Ipatasertib, combined with Temozolomide (TMZ) in cell lines and preclinical animal models.
    RESULTS: GSEA and pathway enrichment analysis indicated that the PI3K/AKT pathway significantly correlated with Nrf2-guided gene expression and ferroptosis-related pathways. Mechanistically, AKT suppresses the activity of GSK3b and stabilizes Nrf2. Moreover, inhibition of AKT activity with ipatasertib synergizes with the genotoxic agent temozolomide, leading to overwhelming ferroptotic cell death in IDH-mutated cancer cells. The preclinical animal model confirmed that combining ipatasertib and TMZ treatment prolonged survival.
    CONCLUSIONS: Our findings highlighted AKT/Nrf2 pathways as a potential synthetic lethality target for IDH mutated cancers.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-22-3179
  8. Cell Syst. 2023 Jan 11. pii: S2405-4712(22)00500-2. [Epub ahead of print]
    Quantifying stimulus-response specificity to probe the functional state of macrophages.
    Katherine M Sheu, Aditya A Guru, Alexander Hoffmann.
      Immune sentinel macrophages initiate responses to pathogens via hundreds of immune response genes. Each immune threat demands a tailored response, suggesting that the capacity for stimulus-specific gene expression is a key functional hallmark of healthy macrophages. To quantify this property, termed "stimulus-response specificity" (SRS), we developed a single-cell experimental workflow and analytical approaches based on information theory and machine learning. We found that the response specificity of macrophages is driven by combinations of specific immune genes that show low cell-to-cell heterogeneity and are targets of separate signaling pathways. The "response specificity profile," a systematic comparison of multiple stimulus-response distributions, was distinctly altered by polarizing cytokines, and it enabled an assessment of the functional state of macrophages. Indeed, the response specificity profile of peritoneal macrophages from old and obese mice showed characteristic differences, suggesting that SRS may be a basis for measuring the functional state of innate immune cells. A record of this paper's transparent peer review process is included in the supplemental information.
    Keywords:  context dependence; gene regulatory mechanisms; information theory; innate immune function; machine learning; macrophage polarization; macrophages; response specificity; sentinel cells
    DOI:  https://doi.org/10.1016/j.cels.2022.12.012
  9. Proc Natl Acad Sci U S A. 2023 Jan 24. 120(4): e2216531120
    Cell survival following direct executioner-caspase activation.
    Maddalena Nano, James A Mondo, Jacob Harwood, Varuzhan Balasanyan, Denise J Montell.
      Executioner-caspase activation has been considered a point-of-no-return in apoptosis. However, numerous studies report survival from caspase activation after treatment with drugs or radiation. An open question is whether cells can recover from direct caspase activation without pro-survival stress responses induced by drugs. To address this question, we engineered a HeLa cell line to express caspase-3 inducibly and combined it with a quantitative caspase activity reporter. While high caspase activity levels killed all cells and very low levels allowed all cells to live, doses of caspase activity sufficient to kill 15 to 30% of cells nevertheless allowed 70 to 85% to survive. At these doses, neither the rate, nor the peak level, nor the total amount of caspase activity could accurately predict cell death versus survival. Thus, cells can survive direct executioner-caspase activation, and variations in cellular state modify the outcome of potentially lethal caspase activity. Such heterogeneities may underlie incomplete tumor cell killing in response to apoptosis-inducing cancer treatments.
    Keywords:  anastasis; apoptosis; effector caspase; predictive power; recovery
    DOI:  https://doi.org/10.1073/pnas.2216531120
  10. Nat Commun. 2023 Jan 19. 14(1): 310
    Phosphosite Scanning reveals a complex phosphorylation code underlying CDK-dependent activation of Hcm1.
    Michelle M Conti, Rui Li, Michelle A Narváez Ramos, Lihua Julie Zhu, Thomas G Fazzio, Jennifer A Benanti.
      Ordered cell cycle progression is coordinated by cyclin dependent kinases (CDKs). CDKs often phosphorylate substrates at multiple sites clustered within disordered regions. However, for most substrates, it is not known which phosphosites are functionally important. We developed a high-throughput approach, Phosphosite Scanning, that tests the importance of each phosphosite within a multisite phosphorylated domain. We show that Phosphosite Scanning identifies multiple combinations of phosphosites that can regulate protein function and reveals specific phosphorylations that are required for phosphorylation at additional sites within a domain. We applied this approach to the yeast transcription factor Hcm1, a conserved regulator of mitotic genes that is critical for accurate chromosome segregation. Phosphosite Scanning revealed a complex CDK-regulatory circuit that mediates Cks1-dependent phosphorylation of key activating sites in vivo. These results illuminate the mechanism of Hcm1 activation by CDK and establish Phosphosite Scanning as a powerful tool for decoding multisite phosphorylated domains.
    DOI:  https://doi.org/10.1038/s41467-023-36035-9
  11. Cell Syst. 2023 Jan 18. pii: S2405-4712(22)00491-4. [Epub ahead of print]14(1): 24-40.e11
    Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition.
    Omer Karin, Eric A Miska, Benjamin D Simons.
      Biological systems can maintain memories over long timescales, with examples including memories in the brain and immune system. It is unknown how functional properties of memory systems, such as memory persistence, can be established by biological circuits. To address this question, we focus on transgenerational epigenetic inheritance in Caenorhabditis elegans. In response to a trigger, worms silence a target gene for multiple generations, resisting strong dilution due to growth and reproduction. Silencing may also be maintained indefinitely upon selection according to silencing levels. We show that these properties imply the fine-tuning of biochemical rates in which the silencing system is positioned near the transition to bistability. We demonstrate that this behavior is consistent with a generic mechanism based on competition for synthesis resources, which leads to self-organization around a critical state with broad silencing timescales. The theory makes distinct predictions and offers insights into the design principles of long-term memory systems.
    Keywords:  biological memory; design principles; dynamical systems; epigenetic memory; mathematical modeling; self organization; self-tuning to criticality; small RNAs; systems biology; transgenerational inheritance
    DOI:  https://doi.org/10.1016/j.cels.2022.12.003
  12. Nat Metab. 2023 Jan 16.
    Hepatic nonvesicular cholesterol transport is critical for systemic lipid homeostasis.
    Xu Xiao, John Paul Kennelly, Alessandra Ferrari, Bethan L Clifford, Emily Whang, Yajing Gao, Kevin Qian, Jaspreet Sandhu, Kelsey E Jarrett, Madelaine C Brearley-Sholto, Alexander Nguyen, Rohith T Nagari, Min Sub Lee, Sicheng Zhang, Thomas A Weston, Stephen G Young, Steven J Bensinger, Claudio J Villanueva, Thomas Q de Aguiar Vallim, Peter Tontonoz.
      In cell models, changes in the 'accessible' pool of plasma membrane (PM) cholesterol are linked with the regulation of endoplasmic reticulum sterol synthesis and metabolism by the Aster family of nonvesicular transporters; however, the relevance of such nonvesicular transport mechanisms for lipid homeostasis in vivo has not been defined. Here we reveal two physiological contexts that generate accessible PM cholesterol and engage the Aster pathway in the liver: fasting and reverse cholesterol transport. During fasting, adipose-tissue-derived fatty acids activate hepatocyte sphingomyelinase to liberate sequestered PM cholesterol. Aster-dependent cholesterol transport during fasting facilitates cholesteryl ester formation, cholesterol movement into bile and very low-density lipoprotein production. During reverse cholesterol transport, high-density lipoprotein delivers excess cholesterol to the hepatocyte PM through scavenger receptor class B member 1. Loss of hepatic Asters impairs cholesterol movement into feces, raises plasma cholesterol levels and causes cholesterol accumulation in peripheral tissues. These results reveal fundamental mechanisms by which Aster cholesterol flux contributes to hepatic and systemic lipid homeostasis.
    DOI:  https://doi.org/10.1038/s42255-022-00722-6
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