bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022–07–31
twenty-one papers selected by
Ralitsa Radostinova Madsen, University College London
  1. PI3K drives the de novo synthesis of coenzyme A from vitamin B5.
  2. Akt protein boosts cancer metabolism through a two-pronged attack.
  3. Hepatic TORC2 Signaling Facilitates Acute Glucagon-Receptor Enhancement of Insulin-Stimulated Glucose Homeostasis in Mice.
  4. Targeting AKT-Dependent Regulation of Antioxidant Defense Sensitizes AKT-E17K Expressing Cancer Cells to Ionizing Radiation.
  5. AKT1 Transcriptomic Landscape in Breast Cancer Cells.
  6. PI3K inhibitors in chronic lymphocytic leukemia: where do we go from here?
  7. An acquired phosphatidylinositol 4-phosphate transport initiates T-cell deterioration and leukemogenesis.
  8. Phenylalanine impairs insulin signaling and inhibits glucose uptake through modification of IRβ.
  9. Low lamin A levels enhance confined cell migration and metastatic capacity in breast cancer.
  10. P21-activated kinase 4 Pak4 maintains embryonic stem cell pluripotency via Akt activation.
  11. PI3K inhibitors in haematological malignancies.
  12. PI3Kδ activity controls plasticity and discriminates between EMT and stemness based on distinct TGFβ signaling.
  13. Repurposing alpelisib, an anti-cancer drug, for the treatment of severe TIE2-mutated venous malformations: Preliminary pharmacokinetics and pharmacodynamic data.
  14. KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data.
  15. Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis.
  16. Beyond controlling cell size: functional analyses of S6K in tumorigenesis.
  17. Manganese is a physiologically relevant TORC1 activator in yeast and mammals.
  18. Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.
  19. The inositol 5-phosphatase INPP5B regulates B cell receptor clustering and signaling.
  20. Monitoring glycolytic dynamics in single cells using a fluorescent biosensor for fructose 1,6-bisphosphate.
  21. TidyMass an object-oriented reproducible analysis framework for LC-MS data.
  1. Nature. 2022 Jul 27.
    PI3K drives the de novo synthesis of coenzyme A from vitamin B5.
    Christian C Dibble, Samuel A Barritt, Grace E Perry, Evan C Lien, Renee C Geck, Sarah E DuBois-Coyne, David Bartee, Thomas T Zengeya, Emily B Cohen, Min Yuan, Benjamin D Hopkins, Jordan L Meier, John G Clohessy, John M Asara, Lewis C Cantley, Alex Toker.
      In response to hormones and growth factors, the class I phosphoinositide-3-kinase (PI3K) signalling network functions as a major regulator of metabolism and growth, governing cellular nutrient uptake, energy generation, reducing cofactor production and macromolecule biosynthesis1. Many of the driver mutations in cancer with the highest recurrence, including in receptor tyrosine kinases, Ras, PTEN and PI3K, pathologically activate PI3K signalling2,3. However, our understanding of the core metabolic program controlled by PI3K is almost certainly incomplete. Here, using mass-spectrometry-based metabolomics and isotope tracing, we show that PI3K signalling stimulates the de novo synthesis of one of the most pivotal metabolic cofactors: coenzyme A (CoA). CoA is the major carrier of activated acyl groups in cells4,5 and is synthesized from cysteine, ATP and the essential nutrient vitamin B5 (also known as pantothenate)6,7. We identify pantothenate kinase 2 (PANK2) and PANK4 as substrates of the PI3K effector kinase AKT8. Although PANK2 is known to catalyse the rate-determining first step of CoA synthesis, we find that the minimally characterized but highly conserved PANK49 is a rate-limiting suppressor of CoA synthesis through its metabolite phosphatase activity. Phosphorylation of PANK4 by AKT relieves this suppression. Ultimately, the PI3K-PANK4 axis regulates the abundance of acetyl-CoA and other acyl-CoAs, CoA-dependent processes such as lipid metabolism and proliferation. We propose that these regulatory mechanisms coordinate cellular CoA supplies with the demands of hormone/growth-factor-driven or oncogene-driven metabolism and growth.
    DOI:  https://doi.org/10.1038/s41586-022-04984-8
  2. Nature. 2022 Jul 27.
    Akt protein boosts cancer metabolism through a two-pronged attack.
    Philipp Poeller, Almut Schulze.
      
    Keywords:  Biochemistry; Cancer; Metabolism
    DOI:  https://doi.org/10.1038/d41586-022-01603-4
  3. Diabetes. 2022 Jul 25. pii: db211018. [Epub ahead of print]
    Hepatic TORC2 Signaling Facilitates Acute Glucagon-Receptor Enhancement of Insulin-Stimulated Glucose Homeostasis in Mice.
    Teayoun Kim, Shelly Nason, Jessica Antipenko, Brian Finan, Anath Shalev, Richard DiMarchi, Kirk M Habegger.
      Long term glucagon receptor (GCGR) agonism is associated with hyperglycemia and glucose intolerance, while acute GCGR agonism enhances whole-body insulin sensitivity and hepatic AKTSer473 phosphorylation. These divergent effects establish a critical gap in knowledge surrounding GCGR action. mTOR Complex 2 (mTORC2) is composed of seven proteins, including RICTOR, which dictates substrate binding and allows for targeting of AKTSer473. We utilized a liver specific Rictor knockout mouse (RictorΔLiver) to investigate whether mTORC2 is necessary for insulin-receptor (INSR) and GCGR crosstalk. RictorΔLiver mice were characterized by impaired Akt signaling and glucose intolerance. Intriguingly, RictorΔLiver mice were also resistant to GCGR-stimulated hyperglycemia. Consistent with our prior report, GCGR agonism increased glucose infusion rate and suppressed hepatic glucose production during hyperinsulinemic-euglycemic clamp of control animals. However, these benefits to insulin sensitivity were ablated in RictorΔLiver mice. We observed diminished AKTSer473 and GSK3α/βSer21/9 phosphorylation in RictorΔLiver mice, whereas phosphorylation of AKTThr308 was unaltered in livers from clamped mice. These signaling effects were replicated in primary hepatocytes isolated from RictorΔLiver and littermate control mice, confirming cell autonomous crosstalk between GCGR and INSR pathways. In summary, our study reveals the necessity of RICTOR, and thus mTORC2, in GCGR-mediated enhancement of liver and whole-body insulin action.
    DOI:  https://doi.org/10.2337/db21-1018
  4. Front Oncol. 2022 ;12 920017
    Targeting AKT-Dependent Regulation of Antioxidant Defense Sensitizes AKT-E17K Expressing Cancer Cells to Ionizing Radiation.
    Isabell Goetting, Safa Larafa, Katharina Eul, Mikhail Kunin, Burkhard Jakob, Johann Matschke, Verena Jendrossek.
      Aberrant activation of the phosphatidyl-inositol-3-kinase/protein kinase B (AKT) pathway has clinical relevance to radiation resistance, but the underlying mechanisms are incompletely understood. Protection against reactive oxygen species (ROS) plays an emerging role in the regulation of cell survival upon irradiation. AKT-dependent signaling participates in the regulation of cellular antioxidant defense. Here, we were interested to explore a yet unknown role of aberrant activation of AKT in regulating antioxidant defense in response to IR and associated radiation resistance. We combined genetic and pharmacologic approaches to study how aberrant activation of AKT impacts cell metabolism, antioxidant defense, and radiosensitivity. Therefore, we used TRAMPC1 (TrC1) prostate cancer cells overexpressing the clinically relevant AKT-variant AKT-E17K with increased AKT activity or wildtype AKT (AKT-WT) and analyzed the consequences of direct AKT inhibition (MK2206) and inhibition of AKT-dependent metabolic enzymes on the levels of cellular ROS, antioxidant capacity, metabolic state, short-term and long-term survival without and with irradiation. TrC1 cells expressing the clinically relevant AKT1-E17K variant were characterized by improved antioxidant defense compared to TrC1 AKT-WT cells and this was associated with increased radiation resistance. The underlying mechanisms involved AKT-dependent direct and indirect regulation of cellular levels of reduced glutathione (GSH). Pharmacologic inhibition of specific AKT-dependent metabolic enzymes supporting defense against oxidative stress, e.g., inhibition of glutathione synthase and glutathione reductase, improved eradication of clonogenic tumor cells, particularly of TrC1 cells overexpressing AKT-E17K. We conclude that improved capacity of TrC1 AKT-E17K cells to balance antioxidant defense with provision of energy and other metabolites upon irradiation compared to TrC1 AKT-WT cells contributes to their increased radiation resistance. Our findings on the importance of glutathione de novo synthesis and glutathione regeneration for radiation resistance of TrC1 AKT-E17K cells offer novel perspectives for improving radiosensitivity in cancer cells with aberrant AKT activity by combining IR with inhibitors targeting AKT-dependent regulation of GSH provision.
    Keywords:  AKT; antioxidant defense; glutathione reductase; glutathione synthase; glycolysis; hexokinase 2; radioresistance
    DOI:  https://doi.org/10.3389/fonc.2022.920017
  5. Cells. 2022 Jul 25. pii: 2290. [Epub ahead of print]11(15):
    AKT1 Transcriptomic Landscape in Breast Cancer Cells.
    Bijesh George, Bin Gui, Rajeswari Raguraman, Aswathy Mary Paul, Harikrishna Nakshatri, Madhavan Radhakrishna Pillai, Rakesh Kumar.
      Overexpression and hyperactivation of the serine/threonine protein kinase B (AKT) pathway is one of the most common cellular events in breast cancer progression. However, the nature of AKT1-specific genome-wide transcriptomic alterations in breast cancer cells and breast cancer remains unknown to this point. Here, we delineate the impact of selective AKT1 knock down using gene-specific siRNAs or inhibiting the AKT activity with a pan-AKT inhibitor VIII on the nature of transcriptomic changes in breast cancer cells using the genome-wide RNA-sequencing analysis. We found that changes in the cellular levels of AKT1 lead to changes in the levels of a set of differentially expressed genes and, in turn, imply resulting AKT1 cellular functions. In addition to an expected positive relationship between the status of AKT1 and co-expressed cellular genes, our study unexpectedly discovered an inherent role of AKT1 in inhibiting the expression of a subset of genes in both unstimulated and growth factor stimulated breast cancer cells. We found that depletion of AKT1 leads to upregulation of a subset of genes-many of which are also found to be downregulated in breast tumors with elevated high AKT1 as well as upregulated in breast tumors with no detectable AKT expression. Representative experimental validation studies in two breast cancer cell lines showed a reasonable concurrence between the expression data from the RNA-sequencing and qRT-PCR or data from ex vivo inhibition of AKT1 activity in cancer patient-derived cells. In brief, findings presented here provide a resource for further understanding of AKT1-dependent modulation of gene expression in breast cancer cells and broaden the scope and significance of AKT1 targets and their functions.
    Keywords:  AKT1; RNA-sequencing; breast cancer; cancer therapeutics; emerging functions and targets; transcriptome
    DOI:  https://doi.org/10.3390/cells11152290
  6. Haematologica. 2022 Jul 28.
    PI3K inhibitors in chronic lymphocytic leukemia: where do we go from here?
    Sigrid S Skanland, Jennifer R Brown.
      Phosphatidylinositol 3-kinase (PI3K) inhibitors are effective in chronic lymphocytic leukemia (CLL). However, the severe toxicity profile associated with the first-generation inhibitors idelalisib and duvelisib, combined with the availability of other more tolerable agents, have limited their use. CLL is still considered incurable, and relapse after treatment, development of resistance, and treatment intolerance are common. It is therefore of interest to optimize the administration of currently approved PI3K inhibitors and to develop next-generation agents to improve tolerability, so that this class of agents will be considered an effective and safe treatment option when needed. These efforts are reflected in the large number of emerging clinical trials with PI3K inhibitors in CLL. Current strategies to overcome treatment limitations include intermittent dosing, which is established for copanlisib and zandelisib and under investigation for duvelisib and parsaclisib. A second strategy is to combine the PI3K inhibitor with another novel agent, either as a continuous regimen or a fixed-duration regimen, to deepen responses. In addition to these approaches, it is of interest to identify higher-resolution actionable biomarkers that can predict treatment responses and toxicity, and inform personalized treatment decisions. Here, we discuss the current status of PI3K inhibitors in CLL, factors limiting the use of currently approved PI3K inhibitors in CLL, current strategies to overcome these limitations, and where to go next.
    DOI:  https://doi.org/10.3324/haematol.2022.281266
  7. Nat Commun. 2022 Jul 29. 13(1): 4390
    An acquired phosphatidylinositol 4-phosphate transport initiates T-cell deterioration and leukemogenesis.
    Wenbin Zhong, Weize Lin, Yingjie Yang, Dan Chen, Xiuye Cao, Mengyang Xu, Guoping Pan, Huanzhao Chen, Jie Zheng, Xiaoqin Feng, Li Hua Yang, Chaofeng Lai, Vesa M Olkkonen, Jun Xu, Shuzhong Cui, Daoguang Yan.
      Lipid remodeling is crucial for malignant cell transformation and tumorigenesis, but the precise molecular processes involved and direct evidences for these in vivo remain elusive. Here, we report that oxysterol-binding protein (OSBP)-related protein 4 L (ORP4L) is expressed in adult T-cell leukemia (ATL) cells but not normal T-cells. In ORP4L knock-in T-cells, ORP4L dimerizes with OSBP to control the shuttling of OSBP between the Golgi apparatus and the plasma membrane (PM) as an exchanger of phosphatidylinositol 4-phosphate [PI(4)P]/cholesterol. The PI(4)P arriving at the PM via this transport machinery replenishes phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] and phosphatidylinositol (3,4,5) trisphosphate [PI(3,4,5)P3] biosynthesis, thus contributing to PI3K/AKT hyperactivation and T-cell deterioration in vitro and in vivo. Disruption of ORP4L and OSBP dimerization disables PI(4)P transport and T-cell leukemogenesis. In summary, we identify a non-vesicular lipid transport machinery between Golgi and PM maintaining the oncogenic signaling competence initiating T-cell deterioration and leukemogenesis.
    DOI:  https://doi.org/10.1038/s41467-022-32104-7
  8. Nat Commun. 2022 Jul 25. 13(1): 4291
    Phenylalanine impairs insulin signaling and inhibits glucose uptake through modification of IRβ.
    Qian Zhou, Wan-Wan Sun, Jia-Cong Chen, Hui-Lu Zhang, Jie Liu, Yan Lin, Peng-Cheng Lin, Bai-Xing Wu, Yan-Peng An, Lin Huang, Wen-Xing Sun, Xin-Wen Zhou, Yi-Ming Li, Yi-Yuan Yuan, Jian-Yuan Zhao, Wei Xu, Shi-Min Zhao.
      Whether amino acids act on cellular insulin signaling remains unclear, given that increased circulating amino acid levels are associated with the onset of type 2 diabetes (T2D). Here, we report that phenylalanine modifies insulin receptor beta (IRβ) and inactivates insulin signaling and glucose uptake. Mice fed phenylalanine-rich chow or phenylalanine-producing aspartame or overexpressing human phenylalanyl-tRNA synthetase (hFARS) develop insulin resistance and T2D symptoms. Mechanistically, FARS phenylalanylate lysine 1057/1079 of IRβ (F-K1057/1079), inactivating IRβ and preventing insulin from promoting glucose uptake by cells. SIRT1 reverse F-K1057/1079 and counteract the insulin-inactivating effects of hFARS and phenylalanine. F-K1057/1079 and SIRT1 levels in white blood cells from T2D patients are positively and negatively correlated with T2D onset, respectively. Blocking F-K1057/1079 with phenylalaninol sensitizes insulin signaling and relieves T2D symptoms in hFARS-transgenic and db/db mice. These findings shed light on the activation of insulin signaling and T2D progression through inhibition of phenylalanylation.
    DOI:  https://doi.org/10.1038/s41467-022-32000-0
  9. Oncogene. 2022 Jul 27.
    Low lamin A levels enhance confined cell migration and metastatic capacity in breast cancer.
    Emily S Bell, Pragya Shah, Noam Zuela-Sopilniak, Dongsung Kim, Alice-Anais Varlet, Julien L P Morival, Alexandra L McGregor, Philipp Isermann, Patricia M Davidson, Joshua J Elacqua, Jonathan N Lakins, Linda Vahdat, Valerie M Weaver, Marcus B Smolka, Paul N Span, Jan Lammerding.
      Aberrations in nuclear size and shape are commonly used to identify cancerous tissue. However, it remains unclear whether the disturbed nuclear structure directly contributes to the cancer pathology or is merely a consequence of other events occurring during tumorigenesis. Here, we show that highly invasive and proliferative breast cancer cells frequently exhibit Akt-driven lower expression of the nuclear envelope proteins lamin A/C, leading to increased nuclear deformability that permits enhanced cell migration through confined environments that mimic interstitial spaces encountered during metastasis. Importantly, increasing lamin A/C expression in highly invasive breast cancer cells reflected gene expression changes characteristic of human breast tumors with higher LMNA expression, and specifically affected pathways related to cell-ECM interactions, cell metabolism, and PI3K/Akt signaling. Further supporting an important role of lamins in breast cancer metastasis, analysis of lamin levels in human breast tumors revealed a significant association between lower lamin A levels, Akt signaling, and decreased disease-free survival. These findings suggest that downregulation of lamin A/C in breast cancer cells may influence both cellular physical properties and biochemical signaling to promote metastatic progression.
    DOI:  https://doi.org/10.1038/s41388-022-02420-9
  10. Stem Cells. 2022 Jul 28. pii: sxac050. [Epub ahead of print]
    P21-activated kinase 4 Pak4 maintains embryonic stem cell pluripotency via Akt activation.
    Fangyuan Cheng, Mingyue Li, Rick Francis Thorne, Guangzhi Liu, Zhang Yuwei, Mian Wu, Lianxin Liu.
      Exploiting the pluripotent properties of embryonic stem cells (ESCs) holds great promise for regenerative medicine. Nevertheless, directing ESC differentiation into specialized cell lineages requires intricate control governed by both intrinsic and extrinsic factors along with the actions of specific signaling networks. Here, we reveal the involvement of the p21-activated kinase 4 (Pak4), a serine/threonine kinase, in sustaining murine ESC (mESC) pluripotency. Pak4 is highly expressed in R1 ESC cells compared with embryonic fibroblast cells and its expression is progressively decreased during differentiation. Manipulations using knockdown and overexpression demonstrated a positive relationship between Pak4 expression and the clonogenic potential of mESCs. Moreover, ectopic Pak4 expression increases reprogramming efficiency of Oct4-Klf4-Sox2-Myc-induced pluripotent stem cells (iPSCs) whereas Pak4-knockdown iPSCs were largely incapable of generating teratomas containing mesodermal, ectodermal and endodermal tissues, indicative of a failure in differentiation. We further establish that Pak4 expression in mESCs is transcriptionally driven by the core pluripotency factor Nanog which recognizes specific binding motifs in the Pak4 proximal promoter region. In turn, the increased levels of Pak4 in mESCs fundamentally act as an upstream activator of the Akt pathway. Pak4 directly binds to and phosphorylates Akt at Ser473 with the resulting Akt activation shown to attenuate downstream GSK3β signaling. Thus, our findings indicate that the Nanog-Pak4-Akt signaling axis is essential for maintaining mESC self-renewal potential with further importance shown during somatic cell reprogramming where Pak4 appears indispensable for multi-lineage specification.
    Keywords:  Akt; Nanog; Pak4; iPSCs; mESCs; pluripotency
    DOI:  https://doi.org/10.1093/stmcls/sxac050
  11. Lancet Oncol. 2022 Aug;pii: S1470-2045(22)00332-1. [Epub ahead of print]23(8): e365
    PI3K inhibitors in haematological malignancies.
    Matthew J Matasar, Florian Hiemeyer, Barrett H Childs, Pier Luigi Zinzani.
      
    DOI:  https://doi.org/10.1016/S1470-2045(22)00332-1
  12. Commun Biol. 2022 Jul 25. 5(1): 740
    PI3Kδ activity controls plasticity and discriminates between EMT and stemness based on distinct TGFβ signaling.
    Jean Agnetti, Vanessa Bou Malham, Christophe Desterke, Nassima Benzoubir, Juan Peng, Sophie Jacques, Souad Rahmouni, Emanuel Di Valentin, Tuan Zea Tan, Didier Samuel, Jean Paul Thiery, Ama Gassama-Diagne.
      The stem cells involved in formation of the complex human body are epithelial cells that undergo apicobasal polarization and form a hollow lumen. Epithelial plasticity manifests as epithelial to mesenchymal transition (EMT), a process by which epithelial cells switch their polarity and epithelial features to adopt a mesenchymal phenotype. The connection between the EMT program and acquisition of stemness is now supported by a substantial number of reports, although what discriminates these two processes remains largely elusive. In this study, based on 3D organoid culture of hepatocellular carcinoma (HCC)-derived cell lines and AAV8-based protein overexpression in the mouse liver, we show that activity modulation of isoform δ of phosphoinositide 3-kinase (PI3Kδ) controls differentiation and discriminates between stemness and EMT by regulating the transforming growth factor β (TGFβ) signaling. This study provides an important tool to control epithelial cell fate and represents a step forward in understanding the development of aggressive carcinoma.
    DOI:  https://doi.org/10.1038/s42003-022-03637-w
  13. Pediatr Blood Cancer. 2022 Jul 25. e29897
    Repurposing alpelisib, an anti-cancer drug, for the treatment of severe TIE2-mutated venous malformations: Preliminary pharmacokinetics and pharmacodynamic data.
    Amandine Remy, Thai Hoa Tran, Josée Dubois, Paul Gavra, Chantal Lapointe, Rochelle Winikoff, Garcia-Bournissen Facundo, Yves Théorêt, Niina Kleiber.
      Extensive venous malformations involving limbs severely impact quality of life, mostly due to chronic pain and functional limitations. But patients can also display coagulopathy with associated risks of life-threatening thromboembolism and bleeding. Available pharmacological treatments (e.g., sirolimus) are not universally effective. Novel therapies are urgently needed for patients with treatment-resistant venous malformations. We report three patients with TIE-2 receptor mutations treated with alpelisib for 6 months (daily dosing: 50 mg for children weighing <50 kg and 100 mg for those >50 kg). Pain was controlled, gait improved, size of the abnormal venous network decreased, and coagulopathy dramatically improved. Drug exposure was highly variable, suggesting that alpelisib dosing should be individualized to patient's characteristics and guided by therapeutic drug monitoring.
    Keywords:  TIE-2 receptor; alpelisib; pediatrics; pharmacokinetics; vascular anomaly; venous malformation
    DOI:  https://doi.org/10.1002/pbc.29897
  14. Nat Commun. 2022 Jul 25. 13(1): 4283
    KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data.
    Sam Crowl, Ben T Jordan, Hamza Ahmed, Cynthia X Ma, Kristen M Naegle.
      Kinase inhibitors as targeted therapies have played an important role in improving cancer outcomes. However, there are still considerable challenges, such as resistance, non-response, patient stratification, polypharmacology, and identifying combination therapy where understanding a tumor kinase activity profile could be transformative. Here, we develop a graph- and statistics-based algorithm, called KSTAR, to convert phosphoproteomic measurements of cells and tissues into a kinase activity score that is generalizable and useful for clinical pipelines, requiring no quantification of the phosphorylation sites. In this work, we demonstrate that KSTAR reliably captures expected kinase activity differences across different tissues and stimulation contexts, allows for the direct comparison of samples from independent experiments, and is robust across a wide range of dataset sizes. Finally, we apply KSTAR to clinical breast cancer phosphoproteomic data and find that there is potential for kinase activity inference from KSTAR to complement the current clinical diagnosis of HER2 status in breast cancer patients.
    DOI:  https://doi.org/10.1038/s41467-022-32017-5
  15. Cell Syst. 2022 Jul 21. pii: S2405-4712(22)00278-2. [Epub ahead of print]
    Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis.
    Long Xiao, Duchangjiang Fan, Huan Qi, Yulin Cong, Zhuo Du.
      Developmental processes are intrinsically robust so as to preserve a normal-like state in response to genetic and environmental fluctuations. However, the robustness and potential phenotypic plasticity of individual developing cells under genetic perturbations remain to be systematically evaluated. Using large-scale gene perturbation, live imaging, lineage tracing, and single-cell phenomics, we quantified the phenotypic landscape of C. elegans embryogenesis in >2,000 embryos following individual knockdown of over 750 conserved genes. We observed that cellular genetic systems are not sufficiently robust to single-gene perturbations across all cells; rather, gene knockdowns frequently induced cellular defects. Dynamic phenotypic analyses revealed many cellular defects to be transient, with cells exhibiting phenotypic plasticity that serves to alleviate, correct, and accommodate the defects. Moreover, potential developmentally related cell modules may buffer the phenotypic effects of individual cell position changes. Our findings reveal non-negligible contributions of cellular plasticity and multicellularity as compensatory strategies to increase developmental robustness.
    Keywords:  C. elegans; cell lineage tracing; cellular plasticity; developmental compensation; developmental robustness; embryogenesis; gene perturbations; live imaging; phenotypic correction; single-cell phenomics
    DOI:  https://doi.org/10.1016/j.cels.2022.07.001
  16. Cell Death Dis. 2022 Jul 25. 13(7): 646
    Beyond controlling cell size: functional analyses of S6K in tumorigenesis.
    Xueji Wu, Wei Xie, Wenxuan Xie, Wenyi Wei, Jianping Guo.
      As a substrate and major effector of the mammalian target of rapamycin complex 1 (mTORC1), the biological functions of ribosomal protein S6 kinase (S6K) have been canonically assigned for cell size control by facilitating mRNA transcription, splicing, and protein synthesis. However, accumulating evidence implies that diverse stimuli and upstream regulators modulate S6K kinase activity, leading to the activation of a plethora of downstream substrates for distinct pathobiological functions. Beyond controlling cell size, S6K simultaneously plays crucial roles in directing cell apoptosis, metabolism, and feedback regulation of its upstream signals. Thus, we comprehensively summarize the emerging upstream regulators, downstream substrates, mouse models, clinical relevance, and candidate inhibitors for S6K and shed light on S6K as a potential therapeutic target for cancers.
    DOI:  https://doi.org/10.1038/s41419-022-05081-4
  17. Elife. 2022 Jul 29. pii: e80497. [Epub ahead of print]11
    Manganese is a physiologically relevant TORC1 activator in yeast and mammals.
    Raffaele Nicastro, Hélène Gaillard, Laura Zarzuela, Marie-Pierre Péli-Gulli, Elisabet Fernández-García, Mercedes Tomé, Néstor García-Rodríguez, Raúl V Durán, Claudio De Virgilio, Ralf Erik Wellinger.
      The essential biometal manganese (Mn) serves as a cofactor for several enzymes that are crucial for the prevention of human diseases. Whether intracellular Mn levels may be sensed and modulate intracellular signaling events has so far remained largely unexplored. The highly conserved target of rapamycin complex 1 (TORC1, mTORC1 in mammals) protein kinase requires divalent metal cofactors such as magnesium (Mg2+) to phosphorylate effectors as part of a homeostatic process that coordinates cell growth and metabolism with nutrient and/or growth factor availability. Here, our genetic approaches reveal that TORC1 activity is stimulated in vivo by elevated cytoplasmic Mn levels, which can be induced by loss of the Golgi-resident Mn2+ transporter Pmr1 and which depend on the natural resistance-associated macrophage protein (NRAMP) metal ion transporters Smf1 and Smf2. Accordingly, genetic interventions that increase cytoplasmic Mn2+ levels antagonize the effects of rapamycin in triggering autophagy, mitophagy, and Rtg1-Rtg3-dependent mitochondrion-to-nucleus retrograde signaling. Surprisingly, our in vitro protein kinase assays uncovered that Mn2+ activates TORC1 substantially better than Mg2+, which is primarily due to its ability to lower the Km for ATP, thereby allowing more efficient ATP coordination in the catalytic cleft of TORC1. These findings, therefore, provide both a mechanism to explain our genetic observations in yeast and a rationale for how fluctuations in trace amounts of Mn can become physiologically relevant. Supporting this notion, TORC1 is also wired to feedback control mechanisms that impinge on Smf1 and Smf2. Finally, we also show that Mn2+-mediated control of TORC1 is evolutionarily conserved in mammals, which may prove relevant for our understanding of the role of Mn in human diseases.
    Keywords:  NRAMP transporter; S. cerevisiae; TORC1; autophagy; biochemistry; chemical biology; genetics; genomics; human; manganese; mitophagy
    DOI:  https://doi.org/10.7554/eLife.80497
  18. Mol Syst Biol. 2022 Jul;18(7): e11036
    Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.
    Martin Garrido-Rodriguez, Katharina Zirngibl, Olga Ivanova, Sebastian Lobentanzer, Julio Saez-Rodriguez.
      Signal transduction governs cellular behavior, and its dysregulation often leads to human disease. To understand this process, we can use network models based on prior knowledge, where nodes represent biomolecules, usually proteins, and edges indicate interactions between them. Several computational methods combine untargeted omics data with prior knowledge to estimate the state of signaling networks in specific biological scenarios. Here, we review, compare, and classify recent network approaches according to their characteristics in terms of input omics data, prior knowledge and underlying methodologies. We highlight existing challenges in the field, such as the general lack of ground truth and the limitations of prior knowledge. We also point out new omics developments that may have a profound impact, such as single-cell proteomics or large-scale profiling of protein conformational changes. We provide both an introduction for interested users seeking strategies to study cell signaling on a large scale and an update for seasoned modelers.
    Keywords:  biological networks; cellular signaling; functional analysis; phosphoproteomics; transcriptomics
    DOI:  https://doi.org/10.15252/msb.202211036
  19. J Cell Biol. 2022 Sep 05. pii: e202112018. [Epub ahead of print]221(9):
    The inositol 5-phosphatase INPP5B regulates B cell receptor clustering and signaling.
    Alaa Droubi, Connor Wallis, Karen E Anderson, Saifur Rahman, Aloka de Sa, Taufiq Rahman, Len R Stephens, Philip T Hawkins, Martin Lowe.
      Upon antigen binding, the B cell receptor (BCR) undergoes clustering to form a signalosome that propagates downstream signaling required for normal B cell development and physiology. BCR clustering is dependent on remodeling of the cortical actin network, but the mechanisms that regulate actin remodeling in this context remain poorly defined. In this study, we identify the inositol 5-phosphatase INPP5B as a key regulator of actin remodeling, BCR clustering, and downstream signaling in antigen-stimulated B cells. INPP5B acts via dephosphorylation of the inositol lipid PI(4,5)P2 that in turn is necessary for actin disassembly, BCR mobilization, and cell spreading on immobilized surface antigen. These effects can be explained by increased actin severing by cofilin and loss of actin linking to the plasma membrane by ezrin, both of which are sensitive to INPP5B-dependent PI(4,5)P2 hydrolysis. INPP5B is therefore a new player in BCR signaling and may represent an attractive target for treatment of B cell malignancies caused by aberrant BCR signaling.
    DOI:  https://doi.org/10.1083/jcb.202112018
  20. Proc Natl Acad Sci U S A. 2022 Aug 02. 119(31): e2204407119
    Monitoring glycolytic dynamics in single cells using a fluorescent biosensor for fructose 1,6-bisphosphate.
    John N Koberstein, Melissa L Stewart, Chadwick B Smith, Andrei I Tarasov, Frances M Ashcroft, Philip J S Stork, Richard H Goodman.
      Cellular metabolism is regulated over space and time to ensure that energy production is efficiently matched with consumption. Fluorescent biosensors are useful tools for studying metabolism as they enable real-time detection of metabolite abundance with single-cell resolution. For monitoring glycolysis, the intermediate fructose 1,6-bisphosphate (FBP) is a particularly informative signal as its concentration is strongly correlated with flux through the whole pathway. Using GFP insertion into the ligand-binding domain of the Bacillus subtilis transcriptional regulator CggR, we developed a fluorescent biosensor for FBP termed HYlight. We demonstrate that HYlight can reliably report the real-time dynamics of glycolysis in living cells and tissues, driven by various metabolic or pharmacological perturbations, alone or in combination with other physiologically relevant signals. Using this sensor, we uncovered previously unknown aspects of β-cell glycolytic heterogeneity and dynamics.
    Keywords:  fructose 1,6-bisphosphate; glycolysis; β-cells
    DOI:  https://doi.org/10.1073/pnas.2204407119
  21. Nat Commun. 2022 Jul 28. 13(1): 4365
    TidyMass an object-oriented reproducible analysis framework for LC-MS data.
    Xiaotao Shen, Hong Yan, Chuchu Wang, Peng Gao, Caroline H Johnson, Michael P Snyder.
      Reproducibility, traceability, and transparency have been long-standing issues for metabolomics data analysis. Multiple tools have been developed, but limitations still exist. Here, we present the tidyMass project ( https://www.tidymass.org/ ), a comprehensive R-based computational framework that can achieve the traceable, shareable, and reproducible workflow needs of data processing and analysis for LC-MS-based untargeted metabolomics. TidyMass is an ecosystem of R packages that share an underlying design philosophy, grammar, and data structure, which provides a comprehensive, reproducible, and object-oriented computational framework. The modular architecture makes tidyMass a highly flexible and extensible tool, which other users can improve and integrate with other tools to customize their own pipeline.
    DOI:  https://doi.org/10.1038/s41467-022-32155-w
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