bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022‒01‒30
seventeen papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute
  1. Treatment of two infants with PIK3CA-related overgrowth spectrum by alpelisib.
  2. Structural investigations of full-length insulin receptor dynamics and signalling.
  3. Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource.
  4. Endosomal cargo recycling mediated by Gpa1 and Phosphatidylinositol-3-Kinase is inhibited by glucose starvation.
  5. Modeling tuberous sclerosis with organoids.
  6. Activated phosphoinositide 3-dinase delta syndrome (APDS): An update.
  7. IQGAP1 scaffolding links Phosphoinositide Kinases to Cytoskeletal Reorganization.
  8. Insulin: The master regulator of glucose metabolism.
  9. Physiological significance of bistable circuit design in metabolic homeostasis: role of integrated insulin-glucagon signalling network.
  10. Adiponectin Deficiency Promotes Endometrial Carcinoma Pathogenesis and Development via Activation of Mitogen-Activated Protein Kinase.
  11. Nucleus segmentation: towards automated solutions.
  12. AKT1 mediates multiple phosphorylation events that functionally promote HSF1 activation.
  13. Protein phosphatase 2A catalytic subunit β suppresses PMA/ionomycin-induced T-cell activation by negatively regulating PI3K/Akt signaling.
  14. Mechanical disruption of E-cadherin complexes with epidermal growth factor receptor actuates growth factor-dependent signaling.
  15. Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity.
  16. Analysis of protein kinases by Phos-tag SDS-PAGE.
  17. PIP2 determines length and stability of primary cilia by balancing membrane turnovers.
  1. J Exp Med. 2022 Mar 07. pii: e20212148. [Epub ahead of print]219(3):
    Treatment of two infants with PIK3CA-related overgrowth spectrum by alpelisib.
    Gabriel Morin, Caroline Degrugillier-Chopinet, Marie Vincent, Antoine Fraissenon, Hélène Aubert, Célia Chapelle, Clément Hoguin, François Dubos, Benoit Catteau, Florence Petit, Aurélie Mezel, Olivia Domanski, Guillaume Herbreteau, Marie Alesandrini, Nathalie Boddaert, Nathalie Boutry, Christine Broissand, Tianxiang Kevin Han, Fabrice Branle, Sabine Sarnacki, Thomas Blanc, Laurent Guibaud, Guillaume Canaud.
      PIK3CA-related overgrowth spectrum (PROS) includes rare genetic conditions due to gain-of-function mutations in the PIK3CA gene. There is no approved medical therapy for patients with PROS, and alpelisib, an approved PIK3CA inhibitor in oncology, showed promising results in preclinical models and in patients. Here, we report for the first time the outcome of two infants with PROS having life-threatening conditions treated with alpelisib (25 mg) and monitored with pharmacokinetics. Patient 1 was an 8-mo-old girl with voluminous vascular malformation. Patient 2 was a 9-mo-old boy presenting with asymmetrical body overgrowth and right hemimegalencephaly with West syndrome. After 12 mo of follow-up, alpelisib treatment was associated with improvement in signs and symptoms, morphological lesions and vascular anomalies in the two patients. No adverse events were reported during the study. In this case series, pharmacological inhibition of PIK3CA with low-dose alpelisib was feasible and associated with clinical improvements, including a smaller size of associated complex tissue malformations and good tolerability.
    DOI:  https://doi.org/10.1084/jem.20212148
  2. J Mol Biol. 2022 Jan 21. pii: S0022-2836(22)00022-5. [Epub ahead of print] 167458
    Structural investigations of full-length insulin receptor dynamics and signalling.
    Jeppe Nielsen, Jakob Brandt, Thomas Boesen, Tina Hummelshøj, Rita Slaaby, Gerd Schluckebier, Poul Nissen.
      Insulin regulates glucose homeostasis via binding and activation of the insulin receptor dimer at two distinct pairs of binding sites 1 and 2. Here, we present cryo-EM studies of full-length human insulin receptor (hIR) in an active state obtained at non-saturating, physiologically relevant insulin conditions. Insulin binds asymmetrically to the receptor under these conditions, occupying up to three of the four possible binding sites. Deletion analysis of the receptor together with site specific peptides and insulin analogs used in binding studies show that both sites 1 and 2 are required for high insulin affinity. We identify a homotypic interaction of the fibronectin type III domain (FnIII-3) of IR resulting in tight interaction of membrane proximal domains of the active, asymmetric receptor dimer. Our results show how insulin binding at two distinct types of sites disrupts the autoinhibited apo-IR dimer and stabilizes the active dimer. We propose an insulin binding and activation mechanism, which is sequential, exhibits negative cooperativity, and is based on asymmetry at physiological insulin concentrations with one to three insulin molecules activating IR.
    Keywords:  insulin; insulin receptor; insulin receptor dimer; insulin receptor dynamics; insulin receptor sites
    DOI:  https://doi.org/10.1016/j.jmb.2022.167458
  3. Genome Biol. 2022 Jan 26. 23(1): 35
    Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource.
    Lisa Dressler, Michele Bortolomeazzi, Mohamed Reda Keddar, Hrvoje Misetic, Giulia Sartini, Amelia Acha-Sagredo, Lucia Montorsi, Neshika Wijewardhane, Dimitra Repana, Joel Nulsen, Jacki Goldman, Marc Pollitt, Patrick Davis, Amy Strange, Karen Ambrose, Francesca D Ciccarelli.
      BACKGROUND: Genetic alterations of somatic cells can drive non-malignant clone formation and promote cancer initiation. However, the link between these processes remains unclear and hampers our understanding of tissue homeostasis and cancer development.RESULTS: Here, we collect a literature-based repertoire of 3355 well-known or predicted drivers of cancer and non-cancer somatic evolution in 122 cancer types and 12 non-cancer tissues. Mapping the alterations of these genes in 7953 pan-cancer samples reveals that, despite the large size, the known compendium of drivers is still incomplete and biased towards frequently occurring coding mutations. High overlap exists between drivers of cancer and non-cancer somatic evolution, although significant differences emerge in their recurrence. We confirm and expand the unique properties of drivers and identify a core of evolutionarily conserved and essential genes whose germline variation is strongly counter-selected. Somatic alteration in even one of these genes is sufficient to drive clonal expansion but not malignant transformation.
    CONCLUSIONS: Our study offers a comprehensive overview of our current understanding of the genetic events initiating clone expansion and cancer revealing significant gaps and biases that still need to be addressed. The compendium of cancer and non-cancer somatic drivers, their literature support, and properties are accessible in the Network of Cancer Genes and Healthy Drivers resource at http://www.network-cancer-genes.org/ .
    Keywords:  Cancer initiation; Driver genes; Somatic evolution; Systems-level properties
    DOI:  https://doi.org/10.1186/s13059-022-02607-z
  4. Mol Biol Cell. 2022 Jan 26. mbcE21040163
    Endosomal cargo recycling mediated by Gpa1 and Phosphatidylinositol-3-Kinase is inhibited by glucose starvation.
    Kamilla Me Laidlaw, Katherine M Paine, Daniel D Bisinski, Grant Calder, Karen Hogg, Sophia Ahmed, Sally James, Peter J O'Toole, Chris MacDonald.
      Cell surface protein trafficking is regulated in response to nutrient availability, with multiple pathways directing surface membrane proteins to the lysosome for degradation in response to suboptimal extracellular nutrients. Internalised protein and lipid cargoes recycle back to the surface efficiently in glucose replete conditions, but this trafficking is attenuated following glucose starvation. We find cells with either reduced or hyperactive phosphatidylinositol 3-kinase (PI3K) activity are defective for recycling. Furthermore, we find the yeast Gα subunit Gpa1, an endosomal PI3K effector, is required for surface recycling of cargoes. Following glucose starvation, mRNA and protein levels of a distinct Gα subunit Gpa2 are elevated following nuclear translocation of Mig1, which inhibits recycling of various cargoes. As Gpa1 and Gpa2 interact at the surface where Gpa2 concentrates during glucose starvation, we propose this disrupts PI3K activity required for recycling, potentially diverting Gpa1 to the surface and interfering with its endosomal role in recycling. In support of this model, glucose starvation and over-expression of Gpa2 alters PI3K endosomal phosphoinositide production. Glucose deprivation therefore triggers a survival mechanism to increase retention of surface cargoes in endosomes and promote their lysosomal degradation.
    DOI:  https://doi.org/10.1091/mbc.E21-04-0163
  5. Science. 2022 Jan 28. 375(6579): 382-383
    Modeling tuberous sclerosis with organoids.
    Rebecca A Ihrie, Elizabeth P Henske.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/science.abn6158
  6. Pediatr Allergy Immunol. 2022 Jan;33 Suppl 27 69-72
    Activated phosphoinositide 3-dinase delta syndrome (APDS): An update.
    Vassilios Lougaris, Caterina Cancrini, Beatrice Rivalta, Riccardo Castagnoli, Giuliana Giardino, Stefano Volpi, Lucia Leonardi, Francesco La Torre, Silvia Federici, Stefania Corrente, Bianca Laura Cinicola, Annarosa Soresina, Gian Luigi Marseglia, Fabio Cardinale.
      Activated phosphoinositide 3-kinase delta syndrome (APDS) is a recently described form of inborn error of immunity (IEI) caused by heterozygous mutations in PIK3CD or PIK3R1 genes, respectively, encoding leukocyte-restricted catalytic p110δ subunit and the ubiquitously expressed regulatory p85 α subunit of the phosphoinositide 3-kinase δ (PI3Kδ). The first described patients with respiratory infections, hypogammaglobulinemia with normal to elevated IgM serum levels, lymphopenia, and lymphoproliferation. Since the original description, it is becoming evident that the onset of disease may be somewhat variable over time, both in terms of age at presentation and in terms of clinical and immunological complications. In many cases, patients are referred to various specialists such as hematologists, rheumatologists, gastroenterologists, and others, before an immunological evaluation is performed, leading to delay in diagnosis, which negatively affects their prognosis. The significant heterogeneity in the clinical and immunological features affecting APDS patients requires awareness among clinicians since good results with p110δ inhibitors have been reported, certainly ameliorating these patients' quality of life and prognosis.
    Keywords:  activated phosphoinositide 3-kinase delta syndrome; clinical research; immune dysregulation; lymphoproliferation; p110δ; p85; primary combined immune deficiency
    DOI:  https://doi.org/10.1111/pai.13634
  7. Biophys J. 2022 Jan 22. pii: S0006-3495(22)00047-9. [Epub ahead of print]
    IQGAP1 scaffolding links Phosphoinositide Kinases to Cytoskeletal Reorganization.
    V Siddartha Yerramilli, Alonzo H Ross, Suzanne Scarlata, Arne Gericke.
      IQGAP1 is a multi-domain scaffold protein that coordinates the direction and impact of multiple signaling pathways by scaffolding its various binding partners. However, the spatial and temporal resolution of IQGAP1 scaffolding remains unclear. Here, we use fluorescence imaging and correlation methods that allow for real time live cell changes in IQGAP1 localization and complex formation during signaling. We find that IQGAP1 and PIPKIγ interact on both the plasma membrane and in cytosol. EGF stimulation, which can initiate cytoskeletal changes, drives the movement of the cytosolic pool towards the plasma membrane to promote cytoskeletal changes. We also observe that a significant population of cytosolic IQGAP1-PIPKIγ complexes localize to early endosomes, and in some instances, form aggregated clusters which become highly mobile upon EGF stimulation. Our imaging studies show that PIPKIγ and PI3K bind simultaneously to IQGAP1 which may accelerate conversion of PI4P to PI(3,4,5)P3 that is required for cytoskeletal changes. Additionally, we find that IQGAP1 is responsible for PIPKIγ association with two proteins associated with cytoskeletal changes, talin and Cdc42, during EGF stimulation. These results directly show that IQGAP1 provides a physical link between phosphoinositides (through PIPKIγ), focal adhesion formation (through talin) and cytoskeletal reorganization (through Cdc42) upon EGF stimulation. Taken together, our results support the importance of IQGAP1 in regulating cell migration by linking phosphoinositide lipid signaling with cytoskeletal reorganization.
    DOI:  https://doi.org/10.1016/j.bpj.2022.01.018
  8. Metabolism. 2022 Jan 20. pii: S0026-0495(22)00020-8. [Epub ahead of print] 155142
    Insulin: The master regulator of glucose metabolism.
    Luke Norton, Chris Shannon, Amalia Gastaldelli, Ralph A DeFronzo.
      Insulin is the master regulator of glucose, lipid, and protein metabolism. Following ingestion of an oral glucose load or mixed meal, the plasma glucose concentration rises, insulin secretion by the beta cells is stimulated and the hyperinsulinemia, working in concert with hyperglycemia, causes: (i) suppression of endogenous (primarily reflects hepatic) glucose production, (ii) stimulation of glucose uptake by muscle, liver, and adipocytes, (iii) inhibition of lipolysis leading to a decline in plasma FFA concentration which contributes to the suppression of hepatic glucose production and augmentation of muscle glucose uptake, and (iv) vasodilation in muscle, which contributes to enhanced muscle glucose disposal. Herein, the integrated physiologic impact of insulin to maintain normal glucose homeostasis is reviewed and the molecular basis of insulin's diverse actions in muscle, liver, adipocytes, and vasculature are discussed.
    Keywords:  Adipocyte; Diabetes; Insulin liver; Muscle; Vasculature
    DOI:  https://doi.org/10.1016/j.metabol.2022.155142
  9. Mol Biol Rep. 2022 Jan 25.
    Physiological significance of bistable circuit design in metabolic homeostasis: role of integrated insulin-glucagon signalling network.
    Manu Tomar, Pramod R Somvanshi, Venkatesh Kareenhalli.
      BACKGROUND: Insulin and glucagon signalling pathways operate in a synchronised manner to regulate metabolic homeostasis in different physiological conditions (like postprandial, fasting & exercise). Non-linear positive feedback loops involving effector molecules such as AKT and PKA in anabolic and catabolic signalling modules have a key role in eliciting bistable response in these networks.METHODS: We have reviewed literature on insulin and glucagon signaling pathways in metabolic regulation along with the relevance of bistability in homeostasis. An ODE-based integrated signalling network model is used to simulate insulin and glucagon resistance conditions. Modifications in homeostatic to anabolic and catabolic switch activation thresholds are analyzed, indicating the effectiveness of insulin and glucagon signalling pathways in normal and diseased conditions.
    RESULTS: Perturbation analysis of the kinetic model provides valuable insights on bistability and its characterization with respect to endocrine inputs. Disturbance in bistability is linked with dysregulation of plasma macronutrient levels (glucose, fatty acids and amino acids) in abnormal conditions like insulin and glucagon resistance, which is associated with obesity, type 2 diabetes mellitus and non-alcoholic fatty liver disease.
    CONCLUSIONS: This article highlights the role of Systems biology approach in explaining plausible mechanisms underlying metabolic abnormalities. It captures essential crosstalk and feedback mechanisms that play a key role in inducing bistable response in a variety of physiological situations, as well as hints at how to reverse insulin and glucagon resistance.
    Keywords:  Bistability; Glucagon; Homeostasis; Insulin; Insulin resistance; Systems biology
    DOI:  https://doi.org/10.1007/s11033-022-07175-w
  10. J Pathol. 2022 Jan 24.
    Adiponectin Deficiency Promotes Endometrial Carcinoma Pathogenesis and Development via Activation of Mitogen-Activated Protein Kinase.
    Yunjing Yan, Hui Shi, Zhenggang Zhao, Shuai Wang, Sujin Zhou, Yunping Mu, Ning Ding, Yimei Lai, Allan Z Zhao, Lixian Cheng, Fanghong Li.
      Obesity is one of the major risk factors for cancer. Clinical studies have demonstrated that circulating levels of adiponectin are inversely correlated not only with the extent of adiposity, but also with the incidence of several types of cancer, chief among which is endometrial cancer (EC). However, thus far, adiponectin remains correlative factor, without definitive evidence to show a causal effect in EC and the potential mechanism(s) involved. To address this issue, we introduced an Apn-null mutation into Pten haploid deficient (Pten+/- ) mice. Pten heterozygous mutation alone led to the development of EC in less than 30% of female mice; however, when combined with Apn-null mutation, the incidence of endometrial lesions rose to at least two-thirds. Although Apn deficiency did not further potentiate the Akt activation caused by Pten mutation, it elevated the phosphorylation of mitogen-activated protein kinase (MAPK) p42/44, indicating activation of the MAPK signaling pathway. Treatment of Apn-/- ;Pten+/- mice with a MEK inhibitor blocked the development of EC. Finally, xenografts of a PTEN proficient human EC cell line grew faster in Apn-deficient mice, whilst an adiponectin receptor agonist reduced xenograft growth of a PTEN-deficient human EC cell line. Thus, reduction of adiponectin activity promotes EC development, at least in the context of Pten mutation, by activating MAPK. This article is protected by copyright. All rights reserved.
    Keywords:  Endometrial cancer; PTEN, MAPK, AdipoRon; adiponectin; obesity
    DOI:  https://doi.org/10.1002/path.5874
  11. Trends Cell Biol. 2022 Jan 20. pii: S0962-8924(21)00251-8. [Epub ahead of print]
    Nucleus segmentation: towards automated solutions.
    Reka Hollandi, Nikita Moshkov, Lassi Paavolainen, Ervin Tasnadi, Filippo Piccinini, Peter Horvath.
      Single nucleus segmentation is a frequent challenge of microscopy image processing, since it is the first step of many quantitative data analysis pipelines. The quality of tracking single cells, extracting features or classifying cellular phenotypes strongly depends on segmentation accuracy. Worldwide competitions have been held, aiming to improve segmentation, and recent years have definitely brought significant improvements: large annotated datasets are now freely available, several 2D segmentation strategies have been extended to 3D, and deep learning approaches have increased accuracy. However, even today, no generally accepted solution and benchmarking platform exist. We review the most recent single-cell segmentation tools, and provide an interactive method browser to select the most appropriate solution.
    Keywords:  deep learning; image processing; microscopy; nucleus segmentation; oncology; single-cell analysis
    DOI:  https://doi.org/10.1016/j.tcb.2021.12.004
  12. FEBS J. 2022 Jan 26.
    AKT1 mediates multiple phosphorylation events that functionally promote HSF1 activation.
    Wen-Cheng Lu, Ramsey Omari, Haimanti Ray, John Wang, Imade Williams, Curteisha Jacobs, Natasha Hockaden, Matthew L Bochman, Richard L Carpenter.
      The heat stress response activates the transcription factor heat shock factor 1 (HSF1), which subsequently upregulates heat shock proteins to maintain the integrity of the proteome. HSF1 activation requires nuclear localization, trimerization, DNA binding, phosphorylation, and gene transactivation. Phosphorylation at S326 is an important regulator of HSF1 transcriptional activity. Phosphorylation at S326 is mediated by AKT1, mTOR, p38, MEK1, and DYRK2. Here, we observed activation of HSF1 by AKT1 independently of mTOR. AKT2 also phosphorylated S326 of HSF1 but showed weak ability to activate HSF1. Similarly, mTOR, p38, MEK1, and DYRK2 all phosphorylated S326 but AKT1 was the most potent activator. Mass spectrometry showed that AKT1 also phosphorylated HSF1 at T142, S230, and T527 in addition to S326 whereas the other kinases did not. Subsequent investigation revealed that phosphorylation at T142 is necessary for HSF1 trimerization and that S230, S326, and T527 are required for HSF1 gene transactivation and recruitment of TFIIB and CDK9. Interestingly, T527 as a phosphorylated residue has not been previously shown and sits in the transactivation domain, further implying a role for this site in HSF1 gene transactivation. This study suggests that HSF1 hyperphosphorylation is targeted and these specific residues have direct function in regulating HSF1 transcriptional activity.
    Keywords:  AKT1; HSF1; heat shock; phosphorylation
    DOI:  https://doi.org/10.1111/febs.16375
  13. FEBS J. 2022 Jan 24.
    Protein phosphatase 2A catalytic subunit β suppresses PMA/ionomycin-induced T-cell activation by negatively regulating PI3K/Akt signaling.
    Rui Gao, Xin Li, Huiying Gao, Ke Zhao, Xian Liu, Jinfang Liu, Qi Wang, Yaxin Zhu, Hui Chen, Shensi Xiang, Yiqun Zhan, Ronghua Yin, Miao Yu, Hongmei Ning, Xiaoming Yang, Changyan Li.
      The precise regulation of the T cell activation process is critical for overall immune homeostasis. Although protein phosphatase 2A (PP2A) is required for T cell development and function, the role of PPP2CB, which is the catalytic subunit β isoform of PP2A, remains unknown. In this study, using a T cell-specific knockout mouse of PPP2CB (PPP2CBfl/fl Lck-Cre+ ), we demonstrated that PPP2CB was dispensable for T cell development in the thymus and peripheral lymphoid organs. Furthermore, PPP2CB deletion did not affect T cell receptor (TCR)-induced T cell activation or cytokine-induced T cell responses; however, it specifically enhanced phorbol myristate acetate (PMA) plus ionomycin-induced T cell activation with increased cellular proliferation, elevated CD69 and CD25 expression, and enhanced cytokines production (IFN-γ, IL-2 and TNF). Mechanistic analyses suggested that the PPP2CB deletion enhanced activation of the PI3K/Akt signaling pathway and Ca2+ flux following stimulation with PMA plus ionomycin. Moreover, the specific PI3K inhibitor rescued the augmented cell activation in PPP2CB deficient T cells. Using a mass spectrometry-based phospho-peptide analysis, we identified potential substrates of PPP2CB during PMA plus ionomycin-induced T cell activation. Collectively, our study provides evidence of the specific role of PPP2CB in controlling PMA plus ionomycin-induced T cell activation.
    Keywords:  PI3K/Akt signaling; PMA plus ionomycin; PPP2CB; T cell activation
    DOI:  https://doi.org/10.1111/febs.16370
  14. Proc Natl Acad Sci U S A. 2022 Jan 25. pii: e2100679119. [Epub ahead of print]119(4):
    Mechanical disruption of E-cadherin complexes with epidermal growth factor receptor actuates growth factor-dependent signaling.
    Brendan Sullivan, Taylor Light, Vinh Vu, Adrian Kapustka, Kalina Hristova, Deborah Leckband.
      Increased intercellular tension is associated with enhanced cell proliferation and tissue growth. Here, we present evidence for a force-transduction mechanism that links mechanical perturbations of epithelial (E)-cadherin (CDH1) receptors to the force-dependent activation of epidermal growth factor receptor (EGFR, ERBB1)-a key regulator of cell proliferation. Here, coimmunoprecipitation studies first show that E-cadherin and EGFR form complexes at the plasma membrane that are disrupted by either epidermal growth factor (EGF) or increased tension on homophilic E-cadherin bonds. Although force on E-cadherin bonds disrupts the complex in the absence of EGF, soluble EGF is required to mechanically activate EGFR at cadherin adhesions. Fully quantified spectral imaging fluorescence resonance energy transfer further revealed that E-cadherin and EGFR directly associate to form a heterotrimeric complex of two cadherins and one EGFR protein. Together, these results support a model in which the tugging forces on homophilic E-cadherin bonds trigger force-activated signaling by releasing EGFR monomers to dimerize, bind EGF ligand, and signal. These findings reveal the initial steps in E-cadherin-mediated force transduction that directly link intercellular force fluctuations to the activation of growth regulatory signaling cascades.
    Keywords:  FRET; MAPK; cadherin; epidermal growth factor receptor; mechanotransduction
    DOI:  https://doi.org/10.1073/pnas.2100679119
  15. Nat Commun. 2022 Jan 25. 13(1): 474
    Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity.
    Rongjie Fu, Wei He, Jinzhuang Dou, Oscar D Villarreal, Ella Bedford, Helen Wang, Connie Hou, Liang Zhang, Yalong Wang, Dacheng Ma, Yiwen Chen, Xue Gao, Martin Depken, Han Xu.
      The specificity of CRISPR/Cas9 genome editing is largely determined by the sequences of guide RNA (gRNA) and the targeted DNA, yet the sequence-dependent rules underlying off-target effects are not fully understood. To systematically explore the sequence determinants governing CRISPR/Cas9 specificity, here we describe a dual-target system to measure the relative cleavage rate between off- and on-target sequences (off-on ratios) of 1902 gRNAs on 13,314 synthetic target sequences, and reveal a set of sequence rules involving 2 factors in off-targeting: 1) a guide-intrinsic mismatch tolerance (GMT) independent of the mismatch context; 2) an "epistasis-like" combinatorial effect of multiple mismatches, which are associated with the free-energy landscape in R-loop formation and are explainable by a multi-state kinetic model. These sequence rules lead to the development of MOFF, a model-based predictor of Cas9-mediated off-target effects. Moreover, the "epistasis-like" combinatorial effect suggests a strategy of allele-specific genome editing using mismatched guides. With the aid of MOFF prediction, this strategy significantly improves the selectivity and expands the application domain of Cas9-based allele-specific editing, as tested in a high-throughput allele-editing screen on 18 cancer hotspot mutations.
    DOI:  https://doi.org/10.1038/s41467-022-28028-x
  16. J Proteomics. 2022 Jan 19. pii: S1874-3919(22)00008-2. [Epub ahead of print]255 104485
    Analysis of protein kinases by Phos-tag SDS-PAGE.
    Yasunori Sugiyama, Yuuki Uezato.
      Protein kinases regulate almost all biological processes including cell proliferation, differentiation, apoptosis, and gene expression. Dysregulation of protein phosphorylation caused by abnormal activity and expression of protein kinases results in the onset of various diseases such as cancer and metabolic syndromes. The activities of a large number of protein kinases are regulated by phosphorylation. Therefore, analysis of the phosphorylation status of protein kinases is important for elucidation of biological phenomena and the pathogenesis of diseases. To investigate protein phosphorylation, phosphate-binding tag molecule "Phos-tag" was developed. In addition, various techniques and tools using Phos-tag such as Phos-tag SDS-PAGE, have been developed for analysis and profiling of protein phosphorylation. Here, we describe the methods and analytical techniques that use Phos-tag for investigation of protein kinase phosphorylation and the applications of phosphorylation analysis. SIGNIFICANCE: Protein kinases play pivotal roles in regulating many biological processes and pathogenesis of diseases. Determination of phosphorylation status of protein kinases can provide the essential information for their activation. This review provides analytical techniques for analysis of phosphorylation status of protein kinases by Phos-tag SDS-PAGE. We believe that this review would help readers to study in kinomics research.
    Keywords:  Kinomics; Phos-tag; Phosphoproteomics; Phosphorylation; Protein kinase
    DOI:  https://doi.org/10.1016/j.jprot.2022.104485
  17. Commun Biol. 2022 Jan 25. 5(1): 93
    PIP2 determines length and stability of primary cilia by balancing membrane turnovers.
    Simon Stilling, Theodoros Kalliakoudas, Hannah Benninghoven-Frey, Takanari Inoue, Björn H Falkenburger.
      Primary cilia are sensory organelles on many postmitotic cells. The ciliary membrane is continuous with the plasma membrane but differs in its phospholipid composition with phosphatidylinositol 4,5-bisposphate (PIP2) being much reduced toward the ciliary tip. In order to determine the functional significance of this difference, we used chemically induced protein dimerization to rapidly synthesize or degrade PIP2 selectively in the ciliary membrane. We observed ciliary fission when PIP2 was synthesized and a growing ciliary length when PIP2 was degraded. Ciliary fission required local actin polymerisation in the cilium, the Rho kinase Rac, aurora kinase A (AurkA) and histone deacetylase 6 (HDAC6). This pathway was previously described for ciliary disassembly before cell cycle re-entry. Activating ciliary receptors in the presence of dominant negative dynamin also increased ciliary PIP2, and the associated vesicle budding required ciliary PIP2. Finally, ciliary shortening resulting from constitutively increased ciliary PIP2 was mediated by the same actin - AurkA - HDAC6 pathway. Taken together, changes in ciliary PIP2 are a unifying point for ciliary membrane stability and turnover. Different stimuli increase ciliary PIP2 to secrete vesicles and reduce ciliary length by a common pathway. The paucity of PIP2 in the distal cilium therefore ensures ciliary stability.
    DOI:  https://doi.org/10.1038/s42003-022-03028-1
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