bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022‒03‒20
twenty papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute
  1. Single serine on TSC2 exerts biased control over mTORC1 activation mediated by ERK1/2 but not Akt.
  2. Rheb regulates nuclear mTORC1 activity independent of farnesylation.
  3. Small integral membrane protein 10 like 1 enhances differentiation of adipose progenitor cells.
  4. Angiocrine polyamine production regulates adiposity.
  5. Integrating adipocyte insulin signaling and metabolism in the multi-omics era.
  6. Enrichment of Tyrosine Phosphorylated Peptides for Quantitative Mass Spectrometry Analysis of RTK Signaling Dynamics.
  7. Porcine cancer models for clinical translation.
  8. Methylene-bridge tryptophan fatty acylation regulates PI3K-AKT signaling and glucose uptake.
  9. CRISPR somatic genome engineering and cancer modeling in the mouse pancreas and liver.
  10. ARAF suppresses ERBB3 expression and metastasis in a subset of lung cancers.
  11. Targeting CDK4 and CDK6 in cancer.
  12. Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression.
  13. PTEN Deletion in Adult Mice Induces Hypoinsulinemia With Concomitant Low Glucose Levels.
  14. Genomic and Transcriptomic Analyses of Prime Editing Guide RNA-Independent Off-Target Effects by Prime Editors.
  15. Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number.
  16. Copper induces cell death by targeting lipoylated TCA cycle proteins.
  17. Time-series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations.
  18. A single-cell atlas of human and mouse white adipose tissue.
  19. Zebrafish imaging reveals TP53 mutation switching oncogene-induced senescence from suppressor to driver in primary tumorigenesis.
  20. PCR-based profiling of transcription factor activity in vivo by a virus-based reporter battery.
  1. Life Sci Alliance. 2022 Jun;pii: e202101169. [Epub ahead of print]5(6):
    Single serine on TSC2 exerts biased control over mTORC1 activation mediated by ERK1/2 but not Akt.
    Brittany L Dunkerly-Eyring, Shi Pan, Miguel Pinilla-Vera, Desirae McKoy, Sumita Mishra, Maria I Grajeda Martinez, Christian U Oeing, Mark J Ranek, David A Kass.
      Tuberous sclerosis complex-2 (TSC2) negatively regulates mammalian target of rapamycin complex 1 (mTORC1), and its activity is reduced by protein kinase B (Akt) and extracellular response kinase (ERK1/2) phosphorylation to activate mTORC1. Serine 1364 (human) on TSC2 bidirectionally modifies mTORC1 activation by pathological growth factors or hemodynamic stress but has no impact on resting activity. We now show this modification biases to ERK1/2 but not Akt-dependent TSC2-mTORC1 activation. Endothelin-1-stimulated mTORC1 requires ERK1/2 activation and is bidirectionally modified by phospho-mimetic (S1364E) or phospho-silenced (S1364A) mutations. However, mTORC1 activation by Akt-dependent stimuli (insulin or PDGF) is unaltered by S1364 modification. Thrombin stimulates both pathways, yet only the ERK1/2 component is modulated by S1364. S1364 also has negligible impact on mTORC1 regulation by energy or nutrient status. In vivo, diet-induced obesity, diabetes, and fatty liver couple to Akt activation and are also unaltered by TSC2 S1364 mutations. This contrasts to prior reports showing a marked impact of both on pathological pressure-stress. Thus, S1364 provides ERK1/2-selective mTORC1 control and a genetic means to modify pathological versus physiological mTOR stimuli.
    DOI:  https://doi.org/10.26508/lsa.202101169
  2. Cell Chem Biol. 2022 Mar 04. pii: S2451-9456(22)00087-3. [Epub ahead of print]
    Rheb regulates nuclear mTORC1 activity independent of farnesylation.
    Yanghao Zhong, Xin Zhou, Kun-Liang Guan, Jin Zhang.
      The small GTPase Ras homolog enriched in brain (Rheb) plays a critical role in activating the mechanistic target of rapamycin complex 1 (mTORC1), a signaling hub that regulates various cellular functions. We recently observed nuclear mTORC1 activity, raising an intriguing question as to how Rheb, which is known to be farnesylated and localized to intracellular membranes, regulates nuclear mTORC1. In this study, we found that active Rheb is present in the nucleus and required for nuclear mTORC1 activity. We showed that inhibition of farnesyltransferase reduced cytosolic, but not nuclear, mTORC1 activity. Furthermore, a farnesylation-deficient Rheb mutant, with preferential nuclear localization and specific lysosome tethering, enables nuclear and cytosolic mTORC1 activities, respectively. These data suggest that non-farnesylated Rheb is capable of interacting with and activating mTORC1, providing mechanistic insights into the molecular functioning of Rheb as well as regulation of the recently observed, active pool of nuclear mTORC1.
    Keywords:  Compartmentation; PTM; TSC; biosensor; lipid modification; mTOR; small GTPase
    DOI:  https://doi.org/10.1016/j.chembiol.2022.02.006
  3. Biochem Biophys Res Commun. 2022 Mar 04. pii: S0006-291X(22)00333-3. [Epub ahead of print]604 57-62
    Small integral membrane protein 10 like 1 enhances differentiation of adipose progenitor cells.
    Michèle Nebe, Stephanie Kehr, Samuel Schmitz, Jana Breitfeld, Judith Lorenz, Diana Le Duc, Peter F Stadler, Jens Meiler, Wieland Kiess, Antje Garten, Anna S Kirstein.
      Small integral membrane protein 10 like 1 (SMIM10L1) was identified by RNA sequencing as the most significantly downregulated gene in Phosphatase and Tensin Homologue (PTEN) knockdown adipose progenitor cells (APCs). PTEN is a tumor suppressor that antagonizes the growth promoting Phosphoinositide 3-kinase (PI3K)/AKT/mechanistic Target of Rapamycin (mTOR) cascade. Diseases caused by germline pathogenic variants in PTEN are summarized as PTEN Hamartoma Tumor Syndrome (PHTS). This overgrowth syndrome is associated with lipoma formation, especially in pediatric patients. The mechanisms underlying this adipose tissue dysfunction remain elusive. We observed that SMIM10L1 downregulation in APCs led to an enhanced adipocyte differentiation in two- and three-dimensional cell culture and increased expression of adipogenesis markers. Furthermore, SMIM10L1 knockdown cells showed a decreased expression of PTEN, pointing to a mutual crosstalk between PTEN and SMIM10L1. In line with these observations, SMIM10L1 knockdown cells showed increased activation of PI3K/AKT/mTOR signaling and concomitantly increased expression of the adipogenic transcription factor SREBP1. We computationally predicted an α-helical structure and membrane association of SMIM10L1. These results support a specific role for SMIM10L1 in regulating adipogenesis, potentially by increasing PI3K/AKT/mTOR signaling, which might be conducive to lipoma formation in pediatric patients with PHTS.
    Keywords:  Adipogenesis; Lipomatosis; PHTS; PTEN Hamartoma tumor syndrome; SMIM10L1
    DOI:  https://doi.org/10.1016/j.bbrc.2022.03.014
  4. Nat Metab. 2022 Mar 14.
    Angiocrine polyamine production regulates adiposity.
    Erika Monelli, Pilar Villacampa, Amaia Zabala-Letona, Anabel Martinez-Romero, Judith Llena, Daniel Beiroa, Leonor Gouveia, Iñigo Chivite, Sebastián Zagmutt, Pau Gama-Perez, Oscar Osorio-Conles, Laia Muixi, Ainara Martinez-Gonzalez, Sandra D Castillo, Natalia Martín-Martín, Pau Castel, Lorea Valcarcel-Jimenez, Irene Garcia-Gonzalez, Josep A Villena, Sonia Fernandez-Ruiz, Dolors Serra, Laura Herrero, Rui Benedito, Pablo Garcia-Roves, Josep Vidal, Paul Cohen, Rubén Nogueiras, Marc Claret, Arkaitz Carracedo, Mariona Graupera.
      Reciprocal interactions between endothelial cells (ECs) and adipocytes are fundamental to maintain white adipose tissue (WAT) homeostasis, as illustrated by the activation of angiogenesis upon WAT expansion, a process that is impaired in obesity. However, the molecular mechanisms underlying the crosstalk between ECs and adipocytes remain poorly understood. Here, we show that local production of polyamines in ECs stimulates adipocyte lipolysis and regulates WAT homeostasis in mice. We promote enhanced cell-autonomous angiogenesis by deleting Pten in the murine endothelium. Endothelial Pten loss leads to a WAT-selective phenotype, characterized by reduced body weight and adiposity in pathophysiological conditions. This phenotype stems from enhanced fatty acid β-oxidation in ECs concomitant with a paracrine lipolytic action on adipocytes, accounting for reduced adiposity. Combined analysis of murine models, isolated ECs and human specimens reveals that WAT lipolysis is mediated by mTORC1-dependent production of polyamines by ECs. Our results indicate that angiocrine metabolic signals are important for WAT homeostasis and organismal metabolism.
    DOI:  https://doi.org/10.1038/s42255-022-00544-6
  5. Trends Biochem Sci. 2022 Mar 15. pii: S0968-0004(22)00050-0. [Epub ahead of print]
    Integrating adipocyte insulin signaling and metabolism in the multi-omics era.
    C Martinez Calejman, W G Doxsey, D J Fazakerley, D A Guertin.
      Insulin stimulates glucose uptake into adipocytes via mTORC2/AKT signaling and GLUT4 translocation and directs glucose carbons into glycolysis, glycerol for TAG synthesis, and de novo lipogenesis. Adipocyte insulin resistance is an early indicator of type 2 diabetes in obesity, a worldwide health crisis. Thus, understanding the interplay between insulin signaling and central carbon metabolism pathways that maintains adipocyte function, blood glucose levels, and metabolic homeostasis is critical. While classically viewed through the lens of individual enzyme-substrate interactions, advances in mass spectrometry are beginning to illuminate adipocyte signaling and metabolic networks on an unprecedented scale, yet this is just the tip of the iceberg. Here, we review how 'omics approaches help to elucidate adipocyte insulin action in cellular time and space.
    Keywords:  glucose; insulin; metabolism; metabolomics; phosphoproteomics; white and brown adipose tissue
    DOI:  https://doi.org/10.1016/j.tibs.2022.02.009
  6. Bio Protoc. 2022 Feb 05. 12(3): e4311
    Enrichment of Tyrosine Phosphorylated Peptides for Quantitative Mass Spectrometry Analysis of RTK Signaling Dynamics.
    Vidyasiri Vemulapalli, Stephen C Blacklow, Steven P Gygi, Alison Erickson.
      Cells sense and respond to mitogens by activating a cascade of signaling events, primarily mediated by tyrosine phosphorylation (pY). Because of its key roles in cellular homeostasis, deregulation of this signaling is often linked to oncogenesis. To understand the mechanisms underlying these signaling pathway aberrations, it is necessary to quantify tyrosine phosphorylation on a global scale in cancer cell models. However, the majority of the protein phosphorylation events occur on serine (86%) and threonine (12%) residues, whereas only 2% of phosphorylation events occur on tyrosine residues ( Olsen et al., 2006 ). The low stoichiometry of tyrosine phosphorylation renders it difficult to quantify cellular pY events comprehensively with high mass accuracy and reproducibility. Here, we describe a detailed protocol for isolating and quantifying tyrosine phosphorylated peptides from drug-perturbed, growth factor-stimulated cancer cells, using immunoaffinity purification and tandem mass tags (TMT) coupled with mass spectrometry.
    Keywords:  Growth factor stimulation; Phosphoproteomics; Phosphotyrosine enrichment; Receptor tyrosine kinases; Signal transduction; Tandem mass tag labeling; Tyrosine phosphorylation
    DOI:  https://doi.org/10.21769/BioProtoc.4311
  7. Nat Rev Cancer. 2022 Mar 17.
    Porcine cancer models for clinical translation.
    Dieter Saur, Angelika Schnieke.
      
    DOI:  https://doi.org/10.1038/s41568-022-00467-0
  8. Cell Rep. 2022 Mar 15. pii: S2211-1247(22)00245-5. [Epub ahead of print]38(11): 110509
    Methylene-bridge tryptophan fatty acylation regulates PI3K-AKT signaling and glucose uptake.
    Song-Hua Hu, Xia-Di He, Ji Nie, Jun-Li Hou, Jiang Wu, Xiao-Yan Liu, Yun Wei, Hui-Ru Tang, Wen-Xing Sun, Shu-Xian Zhou, Yi-Yuan Yuan, Yan-Peng An, Guo-Quan Yan, Yan Lin, Peng-Cheng Lin, Jean J Zhao, Ming-Liang Ye, Jian-Yuan Zhao, Wei Xu, Shi-Min Zhao.
      Protein fatty acylation regulates numerous cell signaling pathways. Polyunsaturated fatty acids (PUFAs) exert a plethora of physiological effects, including cell signaling regulation, with underlying mechanisms to be fully understood. Herein, we report that docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) regulate PI3K-AKT signaling by modifying PDK1 and AKT2. DHA-administered mice exhibit altered phosphorylation of proteins in signaling pathways. Methylene bridge-containing DHA/EPA acylate δ1 carbon of tryptophan 448/543 in PDK1 and tryptophan 414 in AKT2 via free radical pathway, recruit both the proteins to the cytoplasmic membrane, and activate PI3K signaling and glucose uptake in a tryptophan acylation-dependent but insulin-independent manner in cultured cells and in mice. DHA/EPA deplete cytosolic PDK1 and AKT2 and induce insulin resistance. Akt2 knockout in mice abrogates DHA/EPA-induced PI3K-AKT signaling. Our results identify PUFA's methylene bridge tryptophan acylation, a protein fatty acylation that regulates cell signaling and may underlie multifaceted effects of methylene-bridge-containing PUFAs.
    Keywords:  Akt signaling; DHA/EPA; fatty acylation
    DOI:  https://doi.org/10.1016/j.celrep.2022.110509
  9. Nat Protoc. 2022 Mar 14.
    CRISPR somatic genome engineering and cancer modeling in the mouse pancreas and liver.
    Thorsten Kaltenbacher, Jessica Löprich, Roman Maresch, Julia Weber, Sebastian Müller, Rupert Oellinger, Nina Groß, Joscha Griger, Niklas de Andrade Krätzig, Petros Avramopoulos, Deepak Ramanujam, Sabine Brummer, Sebastian A Widholz, Stefanie Bärthel, Chiara Falcomatà, Anja Pfaus, Ahmed Alnatsha, Julia Mayerle, Marc Schmidt-Supprian, Maximilian Reichert, Günter Schneider, Ursula Ehmer, Christian J Braun, Dieter Saur, Stefan Engelhardt, Roland Rad.
      Genetically engineered mouse models (GEMMs) transformed the study of organismal disease phenotypes but are limited by their lengthy generation in embryonic stem cells. Here, we describe methods for rapid and scalable genome engineering in somatic cells of the liver and pancreas through delivery of CRISPR components into living mice. We introduce the spectrum of genetic tools, delineate viral and nonviral CRISPR delivery strategies and describe a series of applications, ranging from gene editing and cancer modeling to chromosome engineering or CRISPR multiplexing and its spatio-temporal control. Beyond experimental design and execution, the protocol describes quantification of genetic and functional editing outcomes, including sequencing approaches, data analysis and interpretation. Compared to traditional knockout mice, somatic GEMMs face an increased risk for mouse-to-mouse variability because of the higher experimental demands of the procedures. The robust protocols described here will help unleash the full potential of somatic genome manipulation. Depending on the delivery method and envisaged application, the protocol takes 3-5 weeks.
    DOI:  https://doi.org/10.1038/s41596-021-00677-0
  10. Sci Adv. 2022 Mar 18. 8(11): eabk1538
    ARAF suppresses ERBB3 expression and metastasis in a subset of lung cancers.
    Juliane Mooz, Kristina Riegel, Hari Ps, Anguraj Sadanandam, Federico Marini, Matthias Klein, Ulrike Werner, Wilfried Roth, Annett Wilken-Schmitz, Irmgard Tegeder, Krishnaraj Rajalingam.
      RAF kinases are highly conserved serine/threonine kinases, and among the three RAF isoforms (ARAF, BRAF, and CRAF), the pathophysiological relevance of ARAF is not well defined. Here, we show that patients with lung cancer exhibit low expression of ARAF, which is associated with lymph node metastasis and poor patient survival. We uncover that depletion of ARAF promotes anchorage-independent growth and metastasis through activation of AKT signaling in a subset of lung cancer cells. We identified that loss of ARAF was associated with an increase in ERBB3 expression in a kinase-independent manner. ARAF suppressed the promoter activity of ERBB3, and reconstitution of ARAF in ARAF-depleted cells led to the reversal of enhanced ERBB3-AKT signaling. Furthermore, ARAF inhibited neuregulin 1 (hNRG1)-mediated AKT activation through controlling ERBB3 expression via the transcription factor KLF5. Our results disclose a critical dual role for ARAF kinase in the negative regulation of ERBB3-AKT signaling, thereby suppressing tumor metastasis.
    DOI:  https://doi.org/10.1126/sciadv.abk1538
  11. Nat Rev Cancer. 2022 Mar 18.
    Targeting CDK4 and CDK6 in cancer.
    Shom Goel, Johann S Bergholz, Jean J Zhao.
      Cyclin-dependent kinase 4 (CDK4) and CDK6 are critical mediators of cellular transition into S phase and are important for the initiation, growth and survival of many cancer types. Pharmacological inhibitors of CDK4/6 have rapidly become a new standard of care for patients with advanced hormone receptor-positive breast cancer. As expected, CDK4/6 inhibitors arrest sensitive tumour cells in the G1 phase of the cell cycle. However, the effects of CDK4/6 inhibition are far more wide-reaching. New insights into their mechanisms of action have triggered identification of new therapeutic opportunities, including the development of novel combination regimens, expanded application to a broader range of cancers and use as supportive care to ameliorate the toxic effects of other therapies. Exploring these new opportunities in the clinic is an urgent priority, which in many cases has not been adequately addressed. Here, we provide a framework for conceptualizing the activity of CDK4/6 inhibitors in cancer and explain how this framework might shape the future clinical development of these agents. We also discuss the biological underpinnings of CDK4/6 inhibitor resistance, an increasingly common challenge in clinical oncology.
    DOI:  https://doi.org/10.1038/s41568-022-00456-3
  12. Cell Syst. 2022 Mar 14. pii: S2405-4712(22)00082-5. [Epub ahead of print]
    Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression.
    Dirk Benzinger, Serguei Ovinnikov, Mustafa Khammash.
      Cells live in constantly changing environments and employ dynamic signaling pathways to transduce information about the signals they encounter. However, the mechanisms by which dynamic signals are decoded into appropriate gene expression patterns remain poorly understood. Here, we devise networked optogenetic pathways that achieve dynamic signal processing functions that recapitulate cellular information processing. Exploiting light-responsive transcriptional regulators with differing response kinetics, we build a falling edge pulse detector and show that this circuit can be employed to demultiplex dynamically encoded signals. We combine this demultiplexer with dCas9-based gene networks to construct pulsatile signal filters and decoders. Applying information theory, we show that dynamic multiplexing significantly increases the information transmission capacity from signal to gene expression state. Finally, we use dynamic multiplexing for precise multidimensional regulation of a heterologous metabolic pathway. Our results elucidate design principles of dynamic information processing and provide original synthetic systems capable of decoding complex signals for biotechnological applications.
    Keywords:  dynamic multiplexing; gene expression regulation; information theory; metabolix engineering; optogenetics; signal decoding; signaling dynamics; synthetic biology; systems biology
    DOI:  https://doi.org/10.1016/j.cels.2022.02.004
  13. Front Endocrinol (Lausanne). 2022 ;13 850214
    PTEN Deletion in Adult Mice Induces Hypoinsulinemia With Concomitant Low Glucose Levels.
    Maria Crespo-Masip, Aurora Pérez-Gómez, Carla Guzmán, Sandra Rayego, Nuria Doladé, Alicia García-Carrasco, Ramiro Jover, José Manuel Valdivielso.
      The PI3K/AKT pathway, negatively regulated by PTEN, plays a paramount role in glucose metabolism regulation due to its activation by the insulin receptor signaling pathway. We generated a PTEN-KO mouse to evaluate the systemic effect of the overactivation of the PI3K/AKT pathway in insulin signaling and glucose homeostasis. Our results demonstrate that PTEN-KO mice show very low glucose levels in the fasted state, which poorly respond to glucose and pyruvate administration. Insulinemia decreased without alterations in pancreatic islets. Among the possible reasons, we uncover the deregulation of the expression of proximal tubule glucose transporter and consequent glycosuria. Moreover, we evidence an altered activation of hepatic gluconeogenesis-related genes. In addition, the expression of several genes related to β-oxidation showed a delayed or even absent response to fasting, suggesting that the lack of PTEN not only impairs glucose metabolism but also slows down the use of lipids as a metabolic fuel. We conclude that the inducible full PTEN-KO mice could be a good model to study the metabolic interactions between glycidic and lipidic metabolism in hypoinsulinemic hypoglycemia and that PTEN could be an important mediator in the disease and/or a potential drug target.
    Keywords:  PI3K/AKT; gluconeogenesis; glucose metabolism; hypoinsulinemic hypoglycemia; lipid metabolism
    DOI:  https://doi.org/10.3389/fendo.2022.850214
  14. CRISPR J. 2022 Mar 14.
    Genomic and Transcriptomic Analyses of Prime Editing Guide RNA-Independent Off-Target Effects by Prime Editors.
    Runze Gao, Zhi-Can Fu, Xiangyang Li, Ying Wang, Jia Wei, Guangye Li, Lijie Wang, Jing Wu, Xingxu Huang, Li Yang, Jia Chen.
      Prime editors (PEs) were developed to induce versatile edits at a guide-specified genomic locus. With all RNA-guided genome editors, guide-dependent off-target (OT) mutations can occur at other sites bearing similarity to the intended target. However, whether PEs carry the additional risk of guide-independent mutations elicited by their unique enzymatic moiety (i.e., reverse transcriptase) has not been examined systematically in mammalian cells. Here, we developed a cost-effective sensitive platform to profile guide-independent OT effects in human cells. We did not observe guide-independent OT mutations in the DNA or RNA of prime editor 3 (PE3)-edited cells, or alterations to their telomeres, endogenous retroelements, alternative splicing events, or gene expression. Together, our results showed undetectable prime editing guide RNA-independent OT effects of PE3 in human cells, suggesting the high editing specificity of its reverse-transcriptase moiety.
    DOI:  https://doi.org/10.1089/crispr.2021.0080
  15. Sci Adv. 2022 Mar 18. 8(11): eabl4598
    Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number.
    Dae Wook Kim, Hyukpyo Hong, Jae Kyoung Kim.
      Identifying the sources of cell-to-cell variability in signaling dynamics is essential to understand drug response variability and develop effective therapeutics. However, it is challenging because not all signaling intermediate reactions can be experimentally measured simultaneously. This can be overcome by replacing them with a single random time delay, but the resulting process is non-Markovian, making it difficult to infer cell-to-cell heterogeneity in reaction rates and time delays. To address this, we developed an efficient and scalable moment-based Bayesian inference method (MBI) with a user-friendly computational package that infers cell-to-cell heterogeneity in the non-Markovian signaling process. We applied MBI to single-cell expression profiles from promoters responding to antibiotics and discovered a major source of cell-to-cell variability in antibiotic stress response: the number of rate-limiting steps in signaling cascades. This knowledge can help identify effective therapies that destroy all pathogenic or cancer cells, and the approach can be applied to precision medicine.
    DOI:  https://doi.org/10.1126/sciadv.abl4598
  16. Science. 2022 Mar 18. 375(6586): 1254-1261
    Copper induces cell death by targeting lipoylated TCA cycle proteins.
    Peter Tsvetkov, Shannon Coy, Boryana Petrova, Margaret Dreishpoon, Ana Verma, Mai Abdusamad, Jordan Rossen, Lena Joesch-Cohen, Ranad Humeidi, Ryan D Spangler, John K Eaton, Evgeni Frenkel, Mustafa Kocak, Steven M Corsello, Svetlana Lutsenko, Naama Kanarek, Sandro Santagata, Todd R Golub.
      Copper is an essential cofactor for all organisms, and yet it becomes toxic if concentrations exceed a threshold maintained by evolutionarily conserved homeostatic mechanisms. How excess copper induces cell death, however, is unknown. Here, we show in human cells that copper-dependent, regulated cell death is distinct from known death mechanisms and is dependent on mitochondrial respiration. We show that copper-dependent death occurs by means of direct binding of copper to lipoylated components of the tricarboxylic acid (TCA) cycle. This results in lipoylated protein aggregation and subsequent iron-sulfur cluster protein loss, which leads to proteotoxic stress and ultimately cell death. These findings may explain the need for ancient copper homeostatic mechanisms.
    DOI:  https://doi.org/10.1126/science.abf0529
  17. Mol Syst Biol. 2022 Mar;18(3): e10588
    Time-series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations.
    Alba Jiménez, Dan Lu, Marian Kalocsay, Matthew J Berberich, Petra Balbi, Ashwini Jambhekar, Galit Lahav.
      The cell stress-responsive transcription factor p53 influences the expression of its target genes and subsequent cellular responses based in part on its dynamics (changes in level over time). The mechanisms decoding p53 dynamics into subsequent target mRNA and protein dynamics remain unclear. We systematically quantified p53 target mRNA and protein expression over time under two p53 dynamical regimes, oscillatory and rising, using RNA-sequencing and TMT mass spectrometry. Oscillatory dynamics allowed for a greater variety of dynamical patterns for both mRNAs and proteins. Mathematical modeling of empirical data revealed three distinct mechanisms that decode p53 dynamics. Specific combinations of these mechanisms at the transcriptional and post-transcriptional levels enabled exclusive induction of proteins under particular dynamics. In addition, rising induction of p53 led to higher induction of proteins regardless of their functional class, including proteins promoting arrest of proliferation, the primary cellular outcome under rising p53. Our results highlight the diverse mechanisms cells employ to distinguish complex transcription factor dynamics to regulate gene expression.
    Keywords:  decoding mechanisms; network motifs; p53 dynamics; proteomics; transcriptomics
    DOI:  https://doi.org/10.15252/msb.202110588
  18. Nature. 2022 Mar 16.
    A single-cell atlas of human and mouse white adipose tissue.
    Margo P Emont, Christopher Jacobs, Adam L Essene, Deepti Pant, Danielle Tenen, Georgia Colleluori, Angelica Di Vincenzo, Anja M Jørgensen, Hesam Dashti, Adam Stefek, Elizabeth McGonagle, Sophie Strobel, Samantha Laber, Saaket Agrawal, Gregory P Westcott, Amrita Kar, Molly L Veregge, Anton Gulko, Harini Srinivasan, Zachary Kramer, Eleanna De Filippis, Erin Merkel, Jennifer Ducie, Christopher G Boyd, William Gourash, Anita Courcoulas, Samuel J Lin, Bernard T Lee, Donald Morris, Adam Tobias, Amit V Khera, Melina Claussnitzer, Tune H Pers, Antonio Giordano, Orr Ashenberg, Aviv Regev, Linus T Tsai, Evan D Rosen.
      White adipose tissue, once regarded as morphologically and functionally bland, is now recognized to be dynamic, plastic and heterogenous, and is involved in a wide array of biological processes including energy homeostasis, glucose and lipid handling, blood pressure control and host defence1. High-fat feeding and other metabolic stressors cause marked changes in adipose morphology, physiology and cellular composition1, and alterations in adiposity are associated with insulin resistance, dyslipidemia and type 2 diabetes2. Here we provide detailed cellular atlases of human and mouse subcutaneous and visceral white fat at single-cell resolution across a range of body weight. We identify subpopulations of adipocytes, adipose stem and progenitor cells, vascular and immune cells and demonstrate commonalities and differences across species and dietary conditions. We link specific cell types to increased risk of metabolic disease and provide an initial blueprint for a comprehensive set of interactions between individual cell types in the adipose niche in leanness and obesity. These data comprise an extensive resource for the exploration of genes, traits and cell types in the function of white adipose tissue across species, depots and nutritional conditions.
    DOI:  https://doi.org/10.1038/s41586-022-04518-2
  19. Nat Commun. 2022 Mar 18. 13(1): 1417
    Zebrafish imaging reveals TP53 mutation switching oncogene-induced senescence from suppressor to driver in primary tumorigenesis.
    Yukinari Haraoka, Yuki Akieda, Yuri Nagai, Chihiro Mogi, Tohru Ishitani.
      Most tumours are thought to arise through oncogenic cell generation followed by additional mutations. How a new oncogenic cell primes tumorigenesis by acquiring additional mutations remains unclear. We show that an additional TP53 mutation stimulates primary tumorigenesis by switching oncogene-induced senescence from a tumour suppressor to a driver. Zebrafish imaging reveals that a newly emerged oncogenic cell with the RasG12V mutation becomes senescent and is eliminated from the epithelia, which is prevented by adding a TP53 gain-of-function mutation (TP53R175H) into RasG12V cells. Surviving RasG12V-TP53R175H double-mutant cells senesce and secrete senescence-associated secretory phenotype (SASP)-related inflammatory molecules that convert neighbouring normal cells into SASP factor-secreting senescent cells, generating a heterogeneous tumour-like cell mass. We identify oncogenic cell behaviours that may control the initial human tumorigenesis step. Ras and TP53 mutations and cellular senescence are frequently detected in human tumours; similar switching may occur during the initial step of human tumorigenesis.
    DOI:  https://doi.org/10.1038/s41467-022-29061-6
  20. iScience. 2022 Mar 18. 25(3): 103927
    PCR-based profiling of transcription factor activity in vivo by a virus-based reporter battery.
    Hitomi Abe, Kentaro Abe.
      Understanding the molecular mechanisms of gene regulation is pivotal for understanding how cells establish and modify their identities and functions. Multiple transcription factors (TFs) coordinate to alter gene expression in cells; however, a method to quantitatively analyze the activity of each TF is lacking, particularly in vivo. Here, we introduce a viral-vector-based TF reporter battery that can be used to simultaneously analyze the activity of multiple TFs, visualized as the TF activity profile (TFAP) obtained by qPCR. We show that the cells possess distinct TFAPs that dynamically change according to experimental manipulation or physiological activity. We report a practical method to obtain the TFAP of a defined cell population and their experience-dependent changes in the mouse brain in vivo. The TFAP obtained by our method will help bridge the information gap between the genome and transcriptome and aid the multi-omics view of understanding the gene regulation system.
    Keywords:  Biological sciences; Biological sciences research methodologies; Biology experimental methods; Cell biology; Methodology in biological sciences; Neuroscience
    DOI:  https://doi.org/10.1016/j.isci.2022.103927
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