bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022‒09‒18
29 papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute
  1. Spatiotemporal control of ERK pulse frequency coordinates fate decisions during mammary acinar morphogenesis.
  2. Sequential conversion of PtdIns3P to PtdIns(3,5)P2 via endosome maturation couples nutrient signaling to lysosome reformation and basal autophagy.
  3. Development of selective inhibitors of phosphatidylinositol 3-kinase C2α.
  4. Brain-enriched RagB isoforms regulate the dynamics of mTORC1 activity through GATOR1 inhibition.
  5. A Rag GTPase dimer code defines the regulation of mTORC1 by amino acids.
  6. Control of cell state transitions.
  7. Nanobodies and chemical cross-links advance the structural and functional analysis of PI3Kα.
  8. Physiological media advance cell culture experiments.
  9. Structural basis for FLCN RagC GAP activation in MiT-TFE substrate-selective mTORC1 regulation.
  10. Quantification of Intracellular Citrate Concentrations with Genetically Encoded Biosensors.
  11. Live-cell imaging in human colonic monolayers reveals ERK waves limit the stem cell compartment to maintain epithelial homeostasis.
  12. Tissue-restricted inhibition of mTOR using chemical genetics.
  13. Cytoskeletal vimentin regulates cell size and autophagy through mTORC1 signaling.
  14. Brain-restricted mTOR inhibition with binary pharmacology.
  15. Combined protein and nucleic acid staining in tissues with PANINI.
  16. Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing.
  17. Glucose-driven TOR-FIE-PRC2 signalling controls plant development.
  18. Control of cell metabolism by the epidermal growth factor receptor.
  19. AKT and SGK kinases regulate cell migration by altering Scar/WAVE complex activation and Arp2/3 complex recruitment.
  20. Rapamycin treatment during development extends life span and health span of male mice and Daphnia magna.
  21. Estradiol production of granulosa cells is unaffected by the physiological mix of non-esterified fatty acids in follicular fluid.
  22. CRISPR/Cas9-Mediated Highly Efficient Gene Targeting in Embryonic Stem Cells for Developing Gene-Manipulated Mouse Models.
  23. Building a healthy mouse model ecosystem to interrogate cancer biology.
  24. Independent phenotypic plasticity axes define distinct obesity sub-types.
  25. Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling.
  26. Adipocyte mesenchymal transition contributes to mammary tumor progression.
  27. Stem cells: Mitochondrial biogenesis links growth and EGFR signaling.
  28. Double-strand break toxicity is chromatin context independent.
  29. Activation of TrkB-Akt signaling rescues deficits in a mouse model of SCA6.
  1. Dev Cell. 2022 Sep 07. pii: S1534-5807(22)00594-9. [Epub ahead of print]
    Spatiotemporal control of ERK pulse frequency coordinates fate decisions during mammary acinar morphogenesis.
    Pascal Ender, Paolo Armando Gagliardi, Maciej Dobrzyński, Agne Frismantiene, Coralie Dessauges, Thomas Höhener, Marc-Antoine Jacques, Andrew R Cohen, Olivier Pertz.
      The signaling events controlling proliferation, survival, and apoptosis during mammary epithelial acinar morphogenesis remain poorly characterized. By imaging single-cell ERK activity dynamics in MCF10A acini, we find that these fates depend on the average frequency of non-periodic ERK pulses. High pulse frequency is observed during initial acinus growth, correlating with rapid cell motility and proliferation. Subsequent decrease in motility correlates with lower ERK pulse frequency and quiescence. Later, during lumen formation, coordinated multicellular ERK waves emerge, correlating with high and low ERK pulse frequencies in outer surviving and inner dying cells, respectively. Optogenetic entrainment of ERK pulses causally connects high ERK pulse frequency with inner cell survival. Acini harboring the PIK3CA H1047R mutation display increased ERK pulse frequency and inner cell survival. Thus, fate decisions during acinar morphogenesis are coordinated by different spatiotemporal modalities of ERK pulse frequency.
    Keywords:  3D imaging; ERK; ERK-KTR; MAPK; MCF10A; PI3K; PIK3CA H1407R; acini; biosensors; mammary epithelial cells; morphogenesis; optogenetics; signaling dynamics
    DOI:  https://doi.org/10.1016/j.devcel.2022.08.008
  2. Autophagy. 2022 Sep 14.
    Sequential conversion of PtdIns3P to PtdIns(3,5)P2 via endosome maturation couples nutrient signaling to lysosome reformation and basal autophagy.
    Samuel J Rodgers, Emily I Jones, Christina A Mitchell, Meagan J McGrath.
      Macroautophagy/autophagy occurs basally under nutrient-rich conditions in most mammalian cells, contributing to protein and organelle quality control, and protection against ageing and neurodegeneration. During autophagy, lysosomes are heavily utilized via their fusion with autophagosomes and must be repopulated to maintain autophagic degradative capacity. During starvation-induced autophagy, lysosomes are generated via de novo biogenesis under the control of TFEB (transcription factor EB), or by the recycling of autolysosome membranes via autophagic lysosome reformation (ALR). However, these lysosome repopulation processes do not operate under nutrient-rich conditions. In our recent study, we identify a sequential phosphoinositide conversion pathway that enables lysosome repopulation under nutrient-rich conditions to facilitate basal autophagy. Phosphatidylinositol-3,4-bisphosphate (PtdIns[3,4]P2) signals generated downstream of phosphoinositide 3-kinase alpha (PI3Kα) during growth factor stimulation are converted to phosphatidylinositol-3-phosphate (PtdIns3P) on endosomes by INPP4B (inositol polyphosphate-4-phosphatase type II B). We show that PtdIns3P is retained as endosomes mature into endolysosomes, and serves as a substrate for PIKFYVE (phosphoinositide kinase, FYVE-type zinc finger containing) to generate phosphatidylinositol-3,5-bisphosphate (PtdIns[3,5]P2) to promote SNX2-dependent lysosome reformation, basal autophagic flux and protein aggregate degradation. Therefore, endosome maturation couples nutrient signaling to lysosome repopulation during basal autophagy by delivering PI3Kα-derived PtdIns3P to endolysosomes for PtdIns(3,5)P2-dependent lysosome reformation.
    Keywords:  INPP4B; PI3Kα; PIKFYVE; endosome; lysosome; phosphoinositides; proteostasis
    DOI:  https://doi.org/10.1080/15548627.2022.2124499
  3. Nat Chem Biol. 2022 Sep 15.
    Development of selective inhibitors of phosphatidylinositol 3-kinase C2α.
    Wen-Ting Lo, Hassane Belabed, Murat Kücükdisli, Juliane Metag, Yvette Roske, Polina Prokofeva, Yohei Ohashi, André Horatscheck, Davide Cirillo, Michael Krauss, Christopher Schmied, Martin Neuenschwander, Jens Peter von Kries, Guillaume Médard, Bernhard Kuster, Olga Perisic, Roger L Williams, Oliver Daumke, Bernard Payrastre, Sonia Severin, Marc Nazaré, Volker Haucke.
      Phosphatidylinositol 3-kinase type 2α (PI3KC2α) and related class II PI3K isoforms are of increasing biomedical interest because of their crucial roles in endocytic membrane dynamics, cell division and signaling, angiogenesis, and platelet morphology and function. Herein we report the development and characterization of PhosphatidylInositol Three-kinase Class twO INhibitors (PITCOINs), potent and highly selective small-molecule inhibitors of PI3KC2α catalytic activity. PITCOIN compounds exhibit strong selectivity toward PI3KC2α due to their unique mode of interaction with the ATP-binding site of the enzyme. We demonstrate that acute inhibition of PI3KC2α-mediated synthesis of phosphatidylinositol 3-phosphates by PITCOINs impairs endocytic membrane dynamics and membrane remodeling during platelet-dependent thrombus formation. PITCOINs are potent and selective cell-permeable inhibitors of PI3KC2α function with potential biomedical applications ranging from thrombosis to diabetes and cancer.
    DOI:  https://doi.org/10.1038/s41589-022-01118-z
  4. Nat Cell Biol. 2022 Sep;24(9): 1407-1421
    Brain-enriched RagB isoforms regulate the dynamics of mTORC1 activity through GATOR1 inhibition.
    Gianluca Figlia, Sandra Müller, Anna M Hagenston, Susanne Kleber, Mykola Roiuk, Jan-Philipp Quast, Nora Ten Bosch, Damian Carvajal Ibañez, Daniela Mauceri, Ana Martin-Villalba, Aurelio A Teleman.
      Mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient availability to appropriately regulate cellular anabolism and catabolism. During nutrient restriction, different organs in an animal do not respond equally, with vital organs being relatively spared. This raises the possibility that mTORC1 is differentially regulated in different cell types, yet little is known about this mechanistically. The Rag GTPases, RagA or RagB bound to RagC or RagD, tether mTORC1 in a nutrient-dependent manner to lysosomes where mTORC1 becomes activated. Although the RagA and B paralogues were assumed to be functionally equivalent, we find here that the RagB isoforms, which are highly expressed in neurons, impart mTORC1 with resistance to nutrient starvation by inhibiting the RagA/B GTPase-activating protein GATOR1. We further show that high expression of RagB isoforms is observed in some tumours, revealing an alternative strategy by which cancer cells can retain elevated mTORC1 upon low nutrient availability.
    DOI:  https://doi.org/10.1038/s41556-022-00977-x
  5. Nat Cell Biol. 2022 Sep;24(9): 1394-1406
    A Rag GTPase dimer code defines the regulation of mTORC1 by amino acids.
    Peter Gollwitzer, Nina Grützmacher, Sabine Wilhelm, Daniel Kümmel, Constantinos Demetriades.
      Amino acid availability controls mTORC1 activity via a heterodimeric Rag GTPase complex that functions as a scaffold at the lysosomal surface, bringing together mTORC1 with its activators and effectors. Mammalian cells express four Rag proteins (RagA-D) that form dimers composed of RagA/B bound to RagC/D. Traditionally, the Rag paralogue pairs (RagA/B and RagC/D) are referred to as functionally redundant, with the four dimer combinations used interchangeably in most studies. Here, by using genetically modified cell lines that express single Rag heterodimers, we uncover a Rag dimer code that determines how amino acids regulate mTORC1. First, RagC/D differentially define the substrate specificity downstream of mTORC1, with RagD promoting phosphorylation of its lysosomal substrates TFEB/TFE3, while both Rags are involved in the phosphorylation of non-lysosomal substrates such as S6K. Mechanistically, RagD recruits mTORC1 more potently to lysosomes through increased affinity to the anchoring LAMTOR complex. Furthermore, RagA/B specify the signalling response to amino acid removal, with RagB-expressing cells maintaining lysosomal and active mTORC1 even upon starvation. Overall, our findings reveal key qualitative differences between Rag paralogues in the regulation of mTORC1, and underscore Rag gene duplication and diversification as a potentially impactful event in mammalian evolution.
    DOI:  https://doi.org/10.1038/s41556-022-00976-y
  6. Nature. 2022 Sep 14.
    Control of cell state transitions.
    Oleksii S Rukhlenko, Melinda Halasz, Nora Rauch, Vadim Zhernovkov, Thomas Prince, Kieran Wynne, Stephanie Maher, Eugene Kashdan, Kenneth MacLeod, Neil O Carragher, Walter Kolch, Boris N Kholodenko.
      Understanding cell state transitions and purposefully controlling them is a longstanding challenge in biology. Here we present cell state transition assessment and regulation (cSTAR), an approach for mapping cell states, modelling transitions between them and predicting targeted interventions to convert cell fate decisions. cSTAR uses omics data as input, classifies cell states, and develops a workflow that transforms the input data into mechanistic models that identify a core signalling network, which controls cell fate transitions by influencing whole-cell networks. By integrating signalling and phenotypic data, cSTAR models how cells manoeuvre in Waddington's landscape1 and make decisions about which cell fate to adopt. Notably, cSTAR devises interventions to control the movement of cells in Waddington's landscape. Testing cSTAR in a cellular model of differentiation and proliferation shows a high correlation between quantitative predictions and experimental data. Applying cSTAR to different types of perturbation and omics datasets, including single-cell data, demonstrates its flexibility and scalability and provides new biological insights. The ability of cSTAR to identify targeted perturbations that interconvert cell fates will enable designer approaches for manipulating cellular development pathways and mechanistically underpinned therapeutic interventions.
    DOI:  https://doi.org/10.1038/s41586-022-05194-y
  7. Proc Natl Acad Sci U S A. 2022 Sep 20. 119(38): e2210769119
    Nanobodies and chemical cross-links advance the structural and functional analysis of PI3Kα.
    Jonathan R Hart, Xiao Liu, Chen Pan, Anyi Liang, Lynn Ueno, Yingna Xu, Alexandra Quezada, Xinyu Zou, Su Yang, Qingtong Zhou, Steve Schoonooghe, Gholamreza Hassanzadeh-Ghassabeh, Tian Xia, Wenqing Shui, Dehua Yang, Peter K Vogt, Ming-Wei Wang.
      Nanobodies and chemical cross-linking were used to gain information on the identity and positions of flexible domains of PI3Kα. The application of chemical cross-linking mass spectrometry (CXMS) facilitated the identification of the p85 domains BH, cSH2, and SH3 as well as their docking positions on the PI3Kα catalytic core. Binding of individual nanobodies to PI3Kα induced activation or inhibition of enzyme activity and caused conformational changes that could be correlated with enzyme function. Binding of nanobody Nb3-126 to the BH domain of p85α substantially improved resolution for parts of the PI3Kα complex, and binding of nanobody Nb3-159 induced a conformation of PI3Kα that is distinct from known PI3Kα structures. The analysis of CXMS data also provided mechanistic insights into the molecular underpinning of the flexibility of PI3Kα.
    Keywords:  chemical cross-linking; conformational changes; mass spectrometry; nanobody; phosphoinositide 3-kinase (PI3K)
    DOI:  https://doi.org/10.1073/pnas.2210769119
  8. Trends Biochem Sci. 2022 Sep 13. pii: S0968-0004(22)00232-8. [Epub ahead of print]
    Physiological media advance cell culture experiments.
    Martin Fischer.
      The metabolism plays a fundamental role in cellular signaling pathways, but commonly used cell culture media do not reflect physiological metabolite concentrations. The metabolic control hub mammalian target of rapamycin complex 1 (mTORC1) kinase is an illuminating example that it is about time to advance our cell culture to become more physiological and relevant.
    Keywords:  RFX7; cancer research; cell culture media; mTOR; metabolism; p53
    DOI:  https://doi.org/10.1016/j.tibs.2022.08.007
  9. Sci Adv. 2022 Sep 16. 8(37): eadd2926
    Structural basis for FLCN RagC GAP activation in MiT-TFE substrate-selective mTORC1 regulation.
    Rachel M Jansen, Roberta Peruzzo, Simon A Fromm, Adam L Yokom, Roberto Zoncu, James H Hurley.
      The mechanistic target of rapamycin complex 1 (mTORC1) regulates cell growth and catabolism in response to nutrients through phosphorylation of key substrates. The tumor suppressor folliculin (FLCN) is a RagC/D guanosine triphosphatase (GTPase)-activating protein (GAP) that regulates mTORC1 phosphorylation of MiT-TFE transcription factors, controlling lysosome biogenesis and autophagy. We determined the cryo-electron microscopy structure of the active FLCN complex (AFC) containing FLCN, FNIP2, the N-terminal tail of SLC38A9, the RagAGDP:RagCGDP.BeFx- GTPase dimer, and the Ragulator scaffold. Relative to the inactive lysosomal FLCN complex structure, FLCN reorients by 90°, breaks contact with RagA, and makes previously unseen contacts with RagC that position its Arg164 finger for catalysis. Disruption of the AFC-specific interfaces of FLCN and FNIP2 with RagC eliminated GAP activity and led to nuclear retention of TFE3, with no effect on mTORC1 substrates S6K or 4E-BP1. The structure provides a basis for regulation of an mTORC1 substrate-specific pathway and a roadmap to discover MiT-TFE family selective mTORC1 antagonists.
    DOI:  https://doi.org/10.1126/sciadv.add2926
  10. Methods Mol Biol. 2023 ;2564 247-258
    Quantification of Intracellular Citrate Concentrations with Genetically Encoded Biosensors.
    Yufeng Zhao, Kei Takahashi-Yamashiro, Yi Shen, Robert E Campbell.
      Citrate is a central intracellular metabolite with roles in a variety of normal and aberrant biological processes. The methods for quantifying citrate concentration in cells can enable the study of the molecular mechanisms of citrate-related biological processes and diseases. Compared to existing analytical methods such as enzymatic assays and mass spectrometry, genetically encoded biosensors based on fluorescent proteins (FPs) offer the advantage of noninvasively tracking intracellular ion and small molecule dynamics with high spatial-temporal resolution. These biosensors are less toxic than chemosensors and can be targeted to specific organelles for subcellular imaging. Here we present a protocol for quantification of cytosolic and mitochondrial citrate in mammalian cells with recently reported genetically encoded biosensors for citrate.
    Keywords:  Biosensor; Citrate; Fluorescent protein; Mammalian cell; Microscopy
    DOI:  https://doi.org/10.1007/978-1-0716-2667-2_12
  11. Elife. 2022 Sep 12. pii: e78837. [Epub ahead of print]11
    Live-cell imaging in human colonic monolayers reveals ERK waves limit the stem cell compartment to maintain epithelial homeostasis.
    Kelvin W Pond, Julia M Morris, Olga Alkhimenok, Reeba P Varghese, Carly C Cabel, Nathan A Ellis, Jayati Chakrabarti, Yana Zavros, Juanita L Merchant, Curtis A Thorne, Andrew L Paek.
      The establishment and maintenance of different cellular compartments in tissues is a universal requirement across all metazoans. Maintaining the correct ratio of cell types in time and space allows tissues to form patterned compartments and perform complex functions. Patterning is especially evident in the human colon, where tissue homeostasis is maintained by stem cells in crypt structures that balance proliferation and differentiation. Here, we developed a human 2D patient derived organoid (PDO) screening platform to study tissue patterning and kinase pathway dynamics in single cells. Using this system, we discovered that waves of ERK signaling induced by apoptotic cells play a critical role in maintaining tissue patterning and homeostasis. If ERK is activated acutely across all cells instead of in wavelike patterns, then tissue patterning and stem cells are lost. Conversely, if ERK activity is inhibited, then stem cells become unrestricted and expand dramatically. This work demonstrates that the colonic epithelium requires coordinated ERK signaling dynamics to maintain patterning and tissue homeostasis. Our work reveals how ERK can antagonize stem cells while supporting cell replacement and the function of the gut.
    Keywords:  cell biology; developmental biology; human
    DOI:  https://doi.org/10.7554/eLife.78837
  12. Proc Natl Acad Sci U S A. 2022 Sep 20. 119(38): e2204083119
    Tissue-restricted inhibition of mTOR using chemical genetics.
    Douglas R Wassarman, Kondalarao Bankapalli, Leo J Pallanck, Kevan M Shokat.
      Mammalian target of rapamycin (mTOR) is a highly conserved eukaryotic protein kinase that coordinates cell growth and metabolism, and plays a critical role in cancer, immunity, and aging. It remains unclear how mTOR signaling in individual tissues contributes to whole-organism processes because mTOR inhibitors, like the natural product rapamycin, are administered systemically and target multiple tissues simultaneously. We developed a chemical-genetic system, termed selecTOR, that restricts the activity of a rapamycin analog to specific cell populations through targeted expression of a mutant FKBP12 protein. This analog has reduced affinity for its obligate binding partner FKBP12, which reduces its ability to inhibit mTOR in wild-type cells and tissues. Expression of the mutant FKBP12, which contains an expanded binding pocket, rescues the activity of this rapamycin analog. Using this system, we show that selective mTOR inhibition can be achieved in Saccharomyces cerevisiae and human cells, and we validate the utility of our system in an intact metazoan model organism by identifying the tissues responsible for a rapamycin-induced developmental delay in Drosophila.
    Keywords:  Drosophila; kinase inhibitor; mTOR; rapamycin; tissue specific
    DOI:  https://doi.org/10.1073/pnas.2204083119
  13. PLoS Biol. 2022 Sep;20(9): e3001737
    Cytoskeletal vimentin regulates cell size and autophagy through mTORC1 signaling.
    Ponnuswamy Mohanasundaram, Leila S Coelho-Rato, Mayank Kumar Modi, Marta Urbanska, Franziska Lautenschläger, Fang Cheng, John E Eriksson.
      The nutrient-activated mTORC1 (mechanistic target of rapamycin kinase complex 1) signaling pathway determines cell size by controlling mRNA translation, ribosome biogenesis, protein synthesis, and autophagy. Here, we show that vimentin, a cytoskeletal intermediate filament protein that we have known to be important for wound healing and cancer progression, determines cell size through mTORC1 signaling, an effect that is also manifested at the organism level in mice. This vimentin-mediated regulation is manifested at all levels of mTOR downstream target activation and protein synthesis. We found that vimentin maintains normal cell size by supporting mTORC1 translocation and activation by regulating the activity of amino acid sensing Rag GTPase. We also show that vimentin inhibits the autophagic flux in the absence of growth factors and/or critical nutrients, demonstrating growth factor-independent inhibition of autophagy at the level of mTORC1. Our findings establish that vimentin couples cell size and autophagy through modulating Rag GTPase activity of the mTORC1 signaling pathway.
    DOI:  https://doi.org/10.1371/journal.pbio.3001737
  14. Nature. 2022 Sep 14.
    Brain-restricted mTOR inhibition with binary pharmacology.
    Ziyang Zhang, Qiwen Fan, Xujun Luo, Kevin Lou, William A Weiss, Kevan M Shokat.
      On-target-off-tissue drug engagement is an important source of adverse effects that constrains the therapeutic window of drug candidates1,2. In diseases of the central nervous system, drugs with brain-restricted pharmacology are highly desirable. Here we report a strategy to achieve inhibition of mammalian target of rapamycin (mTOR) while sparing mTOR activity elsewhere through the use of the brain-permeable mTOR inhibitor RapaLink-1 and the brain-impermeable FKBP12 ligand RapaBlock. We show that this drug combination mitigates the systemic effects of mTOR inhibitors but retains the efficacy of RapaLink-1 in glioblastoma xenografts. We further present a general method to design cell-permeable, FKBP12-dependent kinase inhibitors from known drug scaffolds. These inhibitors are sensitive to deactivation by RapaBlock, enabling the brain-restricted inhibition of their respective kinase targets.
    DOI:  https://doi.org/10.1038/s41586-022-05213-y
  15. STAR Protoc. 2022 Sep 09. pii: S2666-1667(22)00543-3. [Epub ahead of print]3(3): 101663
    Combined protein and nucleic acid staining in tissues with PANINI.
    Addison Deisher, Yao Yu Yeo, Sizun Jiang.
      We present here a detailed protocol for PANINI (protein and nucleic acid in situ imaging), a technique that enables the concurrent staining of protein and nucleic acids in archival tissue sections. PANINI utilizes an optimized antigen retrieval strategy that forgoes protease treatment while retaining high sensitivity of nucleic acid detection down to single genomic events. While the protocol here is geared toward standard fluorescent microscopes with 3-4 available channels, PANINI is compatible with many commercial multiplexed tissue imaging modalities. For complete details on the use and execution of this protocol, please refer to Jiang et al. (2022).
    Keywords:  Cell culture; Immunology; Microscopy; Molecular/Chemical probes; Systems biology
    DOI:  https://doi.org/10.1016/j.xpro.2022.101663
  16. Nat Biotechnol. 2022 Sep 15.
    Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing.
    Sean K Simmons, Gila Lithwick-Yanai, Xian Adiconis, Florian Oberstrass, Nika Iremadze, Kathryn Geiger-Schuller, Pratiksha I Thakore, Chris J Frangieh, Omer Barad, Gilad Almogy, Orit Rozenblatt-Rosen, Aviv Regev, Doron Lipson, Joshua Z Levin.
      Here we introduce a mostly natural sequencing-by-synthesis (mnSBS) method for single-cell RNA sequencing (scRNA-seq), adapted to the Ultima genomics platform, and systematically benchmark it against current scRNA-seq technology. mnSBS uses mostly natural, unmodified nucleotides and only a low fraction of fluorescently labeled nucleotides, which allows for high polymerase processivity and lower costs. We demonstrate successful application in four scRNA-seq case studies of different technical and biological types, including 5' and 3' scRNA-seq, human peripheral blood mononuclear cells from a single individual and in multiplex, as well as Perturb-Seq. Benchmarking shows that results from mnSBS-based scRNA-seq are very similar to those using Illumina sequencing, with minor differences in results related to the position of reads relative to annotated gene boundaries, owing to single-end reads of Ultima being closer to gene ends than reads from Illumina. The method is thus compatible with state-of-the-art scRNA-seq libraries independent of the sequencing technology. We expect mnSBS to be of particular utility for cost-effective large-scale scRNA-seq projects.
    DOI:  https://doi.org/10.1038/s41587-022-01452-6
  17. Nature. 2022 Sep 14.
    Glucose-driven TOR-FIE-PRC2 signalling controls plant development.
    Ruiqiang Ye, Meiyue Wang, Hao Du, Shweta Chhajed, Jin Koh, Kun-Hsiang Liu, Jinwoo Shin, Yue Wu, Lin Shi, Lin Xu, Sixue Chen, Yijing Zhang, Jen Sheen.
      Nutrients and energy have emerged as central modulators of developmental programmes in plants and animals1-3. The evolutionarily conserved target of rapamycin (TOR) kinase is a master integrator of nutrient and energy signalling that controls growth. Despite its key regulatory roles in translation, proliferation, metabolism and autophagy2-5, little is known about how TOR shapes developmental transitions and differentiation. Here we show that glucose-activated TOR kinase controls genome-wide histone H3 trimethylation at K27 (H3K27me3) in Arabidopsis thaliana, which regulates cell fate and development6-10. We identify FERTILIZATION-INDEPENDENT ENDOSPERM (FIE), an indispensable component of Polycomb repressive complex 2 (PRC2), which catalyses H3K27me3 (refs. 6-8,10-12), as a TOR target. Direct phosphorylation by TOR promotes the dynamic translocation of FIE from the cytoplasm to the nucleus. Mutation of the phosphorylation site on FIE abrogates the global H3K27me3 landscape, reprogrammes the transcriptome and disrupts organogenesis in plants. Moreover, glucose-TOR-FIE-PRC2 signalling modulates vernalization-induced floral transition. We propose that this signalling axis serves as a nutritional checkpoint leading to epigenetic silencing of key transcription factor genes that specify stem cell destiny in shoot and root meristems and control leaf, flower and silique patterning, branching and vegetative-to-reproduction transition. Our findings reveal a fundamental mechanism of nutrient signalling in direct epigenome reprogramming, with broad relevance for the developmental control of multicellular organisms.
    DOI:  https://doi.org/10.1038/s41586-022-05171-5
  18. Biochim Biophys Acta Mol Cell Res. 2022 Sep 08. pii: S0167-4889(22)00151-3. [Epub ahead of print] 119359
    Control of cell metabolism by the epidermal growth factor receptor.
    Laura A Orofiamma, Dafne Vural, Costin N Antonescu.
      The epidermal growth factor receptor (EGFR) triggers the activation of many intracellular signals that control cell proliferation, growth, survival, migration, and differentiation. Given its wide expression, EGFR has many functions in development and tissue homeostasis. Some of the cellular outcomes of EGFR signaling involve alterations of specific aspects of cellular metabolism, and alterations of cell metabolism are emerging as driving influences in many physiological and pathophysiological contexts. Here we review the mechanisms by which EGFR regulates cell metabolism, including by modulation of gene expression and protein function leading to control of glucose uptake, glycolysis, biosynthetic pathways branching from glucose metabolism, amino acid metabolism, lipogenesis, and mitochondrial function. We further examine how this regulation of cell metabolism by EGFR may contribute to cell proliferation and differentiation and how EGFR-driven control of metabolism can impact certain diseases and therapy outcomes.
    Keywords:  Cancer; Cell metabolism; Differentiation; Proliferation; Receptor signaling
    DOI:  https://doi.org/10.1016/j.bbamcr.2022.119359
  19. Front Mol Biosci. 2022 ;9 965921
    AKT and SGK kinases regulate cell migration by altering Scar/WAVE complex activation and Arp2/3 complex recruitment.
    Shashi Prakash Singh, Peggy Paschke, Luke Tweedy, Robert H Insall.
      Cell polarity and cell migration both depend on pseudopodia and lamellipodia formation. These are regulated by coordinated signaling acting through G-protein coupled receptors and kinases such as PKB/AKT and SGK, as well as the actin cytoskeletal machinery. Here we show that both Dictyostelium PKB and SGK kinases (encoded by pkbA and pkgB) are dispensable for chemotaxis towards folate. However, both are involved in the regulation of pseudopod formation and thus cell motility. Cells lacking pkbA and pkgB showed a substantial drop in cell speed. Actin polymerization is perturbed in pkbA- and reduced in pkgB- and pkbA-/pkgB- mutants. The Scar/WAVE complex, key catalyst of pseudopod formation, is recruited normally to the fronts of all mutant cells (pkbA-, pkgB- and pkbA-/pkgB-), but is unexpectedly unable to recruit the Arp2/3 complex in cells lacking SGK. Consequently, loss of SGK causes a near-complete loss of normal actin pseudopodia, though this can be rescued by overexpression of PKB. Hence both PKB and SGK are required for correct assembly of F-actin and recruitment of the Arp2/3 complex by the Scar/WAVE complex during pseudopodia formation.
    Keywords:  Arp2/3 complex; Scar/WAVE complex; actin; cell motility; pkbA; pkgB
    DOI:  https://doi.org/10.3389/fmolb.2022.965921
  20. Sci Adv. 2022 Sep 16. 8(37): eabo5482
    Rapamycin treatment during development extends life span and health span of male mice and Daphnia magna.
    Anastasia V Shindyapina, Yongmin Cho, Alaattin Kaya, Alexander Tyshkovskiy, José P Castro, Amy Deik, Juozas Gordevicius, Jesse R Poganik, Clary B Clish, Steve Horvath, Leonid Peshkin, Vadim N Gladyshev.
      Development is tightly connected to aging, but whether pharmacologically targeting development can extend life remains unknown. Here, we subjected genetically diverse UMHET3 mice to rapamycin for the first 45 days of life. The mice grew slower and remained smaller than controls for their entire lives. Their reproductive age was delayed without affecting offspring numbers. The treatment was sufficient to extend the median life span by 10%, with the strongest effect in males, and helped to preserve health as measured by frailty index scores, gait speed, and glucose and insulin tolerance tests. Mechanistically, the liver transcriptome and epigenome of treated mice were younger at the completion of treatment. Analogous to mice, rapamycin exposure during development robustly extended the life span of Daphnia magna and reduced its body size. Overall, the results demonstrate that short-term rapamycin treatment during development is a novel longevity intervention that acts by slowing down development and aging, suggesting that aging may be targeted already early in life.
    DOI:  https://doi.org/10.1126/sciadv.abo5482
  21. J Biol Chem. 2022 Sep 09. pii: S0021-9258(22)00920-6. [Epub ahead of print] 102477
    Estradiol production of granulosa cells is unaffected by the physiological mix of non-esterified fatty acids in follicular fluid.
    Vijay Simha Baddela, Marten Michaelis, Arpna Sharma, Christian Plinski, Torsten Viergutz, Jens Vanselow.
      The ovarian cycle is controlled by circulating levels of the steroid hormone 17-β-estradiol, which is predominantly synthesized by the granulosa cells (GCs) of ovarian follicles. Our earlier studies showed that unsaturated fatty acids (USFs) downregulate and saturated fatty acids (SFAs) upregulate estradiol production in GCs. However, it was unclear whether pituitary gonadotropins induce accumulation of free fatty acids (FFA) in the follicular fluid since follicle-stimulating hormone (FSH) induces and luteinizing hormone (LH) inhibits estradiol production in the mammalian ovary. Interestingly, we show here gas chromatography analysis of follicular fluid revealed no differential accumulation of FFA between pre- and post-LH follicles. We therefore wondered how estradiol production is regulated in the physiological context, as USFs and SFAs are mutually present in the follicular fluid. We thus performed in vitro primary GC cultures with palmitate, palmitoleate, stearate, oleate, linoleate, and alpha-linolenate, representing >80% of the FFA fraction in the follicular fluid, and analyzed 62 different cell culture conditions to understand the regulation of estradiol biosynthesis under diverse FFA combinations. Our analyses showed co-supplementation of SFAs with USFs rescued estradiol production by restoring gonadotropin receptors and aromatase, antagonizing the inhibitory effects of USFs. Furthermore, transcriptome data of oleic acid-treated GCs indicated USFs induce the ERK and Akt signaling pathways. We show SFAs inhibit USF-induced ERK1/2 and Akt activation, wherein ERK1/2 acts as a negative regulator of estradiol synthesis. We propose SFAs are vital components of the follicular fluid, without which gonadotropin signaling and the ovarian cycle would probably be shattered by USFs.
    Keywords:  ERK1/2; Estradiol; Gonadotropins; Granulosa cells; NEFAs
    DOI:  https://doi.org/10.1016/j.jbc.2022.102477
  22. J Vis Exp. 2022 Aug 24.
    CRISPR/Cas9-Mediated Highly Efficient Gene Targeting in Embryonic Stem Cells for Developing Gene-Manipulated Mouse Models.
    Manabu Ozawa, Chihiro Emori, Masahito Ikawa.
      The CRISPR/Cas9 system has made it possible to develop genetically modified mice by direct genome editing using fertilized zygotes. However, although the efficiency in developing gene-knockout mice by inducing small indel mutation would be sufficient enough, the efficiency of embryo genome editing for making large-size DNA knock-in (KI) is still low. Therefore, in contrast to the direct KI method in embryos, gene targeting using embryonic stem cells (ESCs) followed by embryo injection to develop chimera mice still has several advantages (e.g., high throughput targeting in vitro, multi-allele manipulation, and Cre and flox gene manipulation can be carried out in a short period). In addition, strains with difficult-to-handle embryos in vitro, such as BALB/c, can also be used for ESC targeting. This protocol describes the optimized method for large-size DNA (several kb) KI in ESCs by applying CRISPR/Cas9-mediated genome editing followed by chimera mice production to develop gene-manipulated mouse models.
    DOI:  https://doi.org/10.3791/64385
  23. Dis Model Mech. 2022 Sep 01. pii: dmm049795. [Epub ahead of print]15(9):
    Building a healthy mouse model ecosystem to interrogate cancer biology.
    Ryan Devlin, Ed Roberts.
      In a recent study, Sargent et al. characterise several novel Rag1-/- mouse strains and demonstrate that genetic background strongly influences xenograft development and phenotype. Here, we discuss this work within the broader context of cancer mouse modelling. We argue that new technologies will enable insights into how specific models align with human disease states and that this knowledge can be used to develop a diverse ecosystem of complementary mouse models of cancer. By utilising these diverse, well-characterised models to provide multiple perspectives on specific cancers, it should be possible to reduce the inappropriate attrition of sound hypotheses while protecting against false positives. Furthermore, careful re-introduction of biological variation, be that through outbred populations, environmental diversity or including animals of both sexes, can ensure that results are more broadly applicable and are less impacted by particular traits of homogeneous experimental populations. Thus, careful characterisation and judicious use of an array of mouse models provides an opportunity to address some of the issues surrounding both the reproducibility and translatability crises often referenced in pre-clinical cancer research.
    DOI:  https://doi.org/10.1242/dmm.049795
  24. Nat Metab. 2022 Sep 12.
    Independent phenotypic plasticity axes define distinct obesity sub-types.
    PERMUTE
      Studies in genetically 'identical' individuals indicate that as much as 50% of complex trait variation cannot be traced to genetics or to the environment. The mechanisms that generate this 'unexplained' phenotypic variation (UPV) remain largely unknown. Here, we identify neuronatin (NNAT) as a conserved factor that buffers against UPV. We find that Nnat deficiency in isogenic mice triggers the emergence of a bi-stable polyphenism, where littermates emerge into adulthood either 'normal' or 'overgrown'. Mechanistically, this is mediated by an insulin-dependent overgrowth that arises from histone deacetylase (HDAC)-dependent β-cell hyperproliferation. A multi-dimensional analysis of monozygotic twin discordance reveals the existence of two patterns of human UPV, one of which (Type B) phenocopies the NNAT-buffered polyphenism identified in mice. Specifically, Type-B monozygotic co-twins exhibit coordinated increases in fat and lean mass across the body; decreased NNAT expression; increased HDAC-responsive gene signatures; and clinical outcomes linked to insulinemia. Critically, the Type-B UPV signature stratifies both childhood and adult cohorts into four metabolic states, including two phenotypically and molecularly distinct types of obesity.
    DOI:  https://doi.org/10.1038/s42255-022-00629-2
  25. Nat Commun. 2022 Sep 16. 13(1): 5439
    Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling.
    András Zeke, Tamás Takács, Péter Sok, Krisztina Németh, Klára Kirsch, Péter Egri, Ádám Levente Póti, Isabel Bento, Gábor E Tusnády, Attila Reményi.
      Serine/threonine phosphorylation of insulin receptor substrate (IRS) proteins is well known to modulate insulin signaling. However, the molecular details of this process have mostly been elusive. While exploring the role of phosphoserines, we have detected a direct link between Tyr-flanking Ser/Thr phosphorylation sites and regulation of specific phosphotyrosine phosphatases. Here we present a concise structural study on how the activity of SHP2 phosphatase is controlled by an asymmetric, dual phosphorylation of its substrates. The structure of SHP2 has been determined with three different substrate peptides, unveiling the versatile and highly dynamic nature of substrate recruitment. What is more, the relatively stable pre-catalytic state of SHP2 could potentially be useful for inhibitor design. Our findings not only show an unusual dependence of SHP2 catalytic activity on Ser/Thr phosphorylation sites in IRS1 and CD28, but also suggest a negative regulatory mechanism that may also apply to other tyrosine kinase pathways as well.
    DOI:  https://doi.org/10.1038/s41467-022-32918-5
  26. Cell Rep. 2022 Sep 13. pii: S2211-1247(22)01194-9. [Epub ahead of print]40(11): 111362
    Adipocyte mesenchymal transition contributes to mammary tumor progression.
    Qingzhang Zhu, Yi Zhu, Chelsea Hepler, Qianbin Zhang, Jiyoung Park, Christy Gliniak, Gervaise H Henry, Clair Crewe, Dawei Bu, Zhuzhen Zhang, Shangang Zhao, Thomas Morley, Na Li, Dae-Seok Kim, Douglas Strand, Yingfeng Deng, Jacob J Robino, Oleg Varlamov, Ruth Gordillo, Mikhail G Kolonin, Christine M Kusminski, Rana K Gupta, Philipp E Scherer.
      Obesity is associated with increased cancer incidence and progression. However, the relationship between adiposity and cancer remains poorly understood at the mechanistic level. Here, we report that adipocytes from tumor-invasive mammary fat undergo de-differentiation to fibroblast-like precursor cells during tumor progression and integrate into the tumor microenvironment. Single-cell sequencing reveals that these de-differentiated adipocytes lose their original identities and transform into multiple cell types, including myofibroblast- and macrophage-like cells, with their characteristic features involved in immune response, inflammation, and extracellular matrix remodeling. The de-differentiated cells are metabolically distinct from tumor-associated fibroblasts but exhibit comparable effects on tumor cell proliferation. Inducing de-differentiation by Xbp1s overexpression promotes tumor progression despite lower adiposity. In contrast, promoting lipid-storage capacity in adipocytes through MitoNEET overexpression curbs tumor growth despite greater adiposity. Collectively, the metabolic interplay between tumor cells and adipocytes induces adipocyte mesenchymal transition and contributes to reconfigure the stroma into a more tumor-friendly microenvironment.
    Keywords:  CP: Cancer; CP: Metabolism; adipocyte; breast cancer; de-differentiation; obesity
    DOI:  https://doi.org/10.1016/j.celrep.2022.111362
  27. Curr Biol. 2022 Sep 12. pii: S0960-9822(22)01234-9. [Epub ahead of print]32(17): R931-R934
    Stem cells: Mitochondrial biogenesis links growth and EGFR signaling.
    Louis Gervais, Allison J Bardin.
      Epidermal growth factor receptor signaling is central to cell proliferation, growth, and survival and is often deregulated in cancers. A new study links downstream effectors of this receptor to stem cell growth via mitochondrial biogenesis and metabolic reprogramming.
    DOI:  https://doi.org/10.1016/j.cub.2022.08.002
  28. Nucleic Acids Res. 2022 Sep 15. pii: gkac758. [Epub ahead of print]
    Double-strand break toxicity is chromatin context independent.
    Anoek Friskes, Lisa Koob, Lenno Krenning, Tesa M Severson, Emma S Koeleman, Xabier Vergara, Michael Schubert, Jeroen van den Berg, Bastiaan Evers, Anna G Manjón, Stacey Joosten, Yongsoo Kim, Wilbert Zwart, René H Medema.
      Cells respond to double-strand breaks (DSBs) by activating DNA damage response pathways, including cell cycle arrest. We have previously shown that a single double-strand break generated via CRISPR/Cas9 is sufficient to delay cell cycle progression and compromise cell viability. However, we also found that the cellular response to DSBs can vary, independent of the number of lesions. This implies that not all DSBs are equally toxic, and raises the question if the location of a single double-strand break could influence its toxicity. To systematically investigate if DSB-location is a determinant of toxicity we performed a CRISPR/Cas9 screen targeting 6237 single sites in the human genome. Next, we developed a data-driven framework to design CRISPR/Cas9 sgRNA (crRNA) pools targeting specific chromatin features. The chromatin context was defined using ChromHMM states, Lamin-B1 DAM-iD, DNAseI hypersensitivity, and RNA-sequencing data. We computationally designed 6 distinct crRNA pools, each containing 10 crRNAs targeting the same chromatin state. We show that the toxicity of a DSB is highly similar across the different ChromHMM states. Rather, we find that the major determinants of toxicity of a sgRNA are cutting efficiency and off-target effects. Thus, chromatin features have little to no effect on the toxicity of a single CRISPR/Cas9-induced DSB.
    DOI:  https://doi.org/10.1093/nar/gkac758
  29. Sci Adv. 2022 Sep 16. 8(37): eabh3260
    Activation of TrkB-Akt signaling rescues deficits in a mouse model of SCA6.
    Anna A Cook, Sriram Jayabal, Jacky Sheng, Eviatar Fields, Tsz Chui Sophia Leung, Sabrina Quilez, Eileen McNicholas, Lois Lau, Shixia Huang, Alanna J Watt.
      Spinocerebellar ataxia type 6 (SCA6) is a neurodegenerative disease resulting in motor coordination deficits and cerebellar pathology. Expression of brain-derived neurotrophic factor (BDNF) is reduced in postmortem tissue from SCA6 patients. Here, we show that levels of cerebellar BDNF and its receptor, tropomyosin receptor kinase B (TrkB), are reduced at an early disease stage in a mouse model of SCA6 (SCA684Q/84Q). One month of exercise elevated cerebellar BDNF expression and improved ataxia and cerebellar Purkinje cell firing rate deficits. A TrkB agonist, 7,8-dihydroxyflavone (7,8-DHF), likewise improved motor coordination and Purkinje cell firing rate and elevated downstream Akt signaling. Prolonged 7,8-DHF administration persistently improved ataxia when treatment commenced near disease onset but was ineffective when treatment was started late. These data suggest that 7,8-DHF, which is orally bioavailable and crosses the blood-brain barrier, is a promising therapeutic for SCA6 and argue for the importance of early intervention for SCA6.
    DOI:  https://doi.org/10.1126/sciadv.abh3260
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