bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023–03–12
twenty-one papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Making single-cell proteomics biologically relevant.
  2. Roles of PI3Kγ and PI3Kδ in mantle cell lymphoma proliferation and migration contributing to efficacy of the PI3Kγ/δ inhibitor duvelisib.
  3. On the inference of ERK signaling dynamics from protein biosensor measurements.
  4. Altered DNA repair pathway engagement by engineered CRISPR-Cas9 nucleases.
  5. Analysis of context-specific KRAS-effector (sub)complexes in Caco-2 cells.
  6. oFlowSeq: a quantitative approach to identify protein coding mutations affecting cell type enrichment using mosaic CRISPR-Cas9 edited cerebral organoids.
  7. Characterization of p38α signaling networks in cancer cells using quantitative proteomics and phosphoproteomics.
  8. Sampling the proteome by emerging single-molecule and mass spectrometry methods.
  9. Single-cell proteomics: challenges and prospects.
  10. Phosphorylation of LKB1 by PDK1 Inhibits Cell Proliferation and Organ Growth by Decreased Activation of AMPK.
  11. Microfluidics-free single-cell genomics with templated emulsification.
  12. Non-canonical functions of SNAIL drive context-specific cancer progression.
  13. Temporal phosphoproteomic analysis of VEGF-A signaling in HUVECs: an insight into early signaling events associated with angiogenesis.
  14. Sniper2L is a high-fidelity Cas9 variant with high activity.
  15. We need a plan D.
  16. Mass Spectrometry Imaging Reveals Early Metabolic Priming of Cell Lineage in Differentiating Human-Induced Pluripotent Stem Cells.
  17. Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase.
  18. A chemically controlled Cas9 switch enables temporal modulation of diverse effectors.
  19. Not if but when nanopore protein sequencing meets single-cell proteomics.
  20. Physiologically relevant culture medium Plasmax improves human placental trophoblast stem cell function.
  21. Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput.
  1. Nat Methods. 2023 Mar;20(3): 320-323
    Making single-cell proteomics biologically relevant.
    Florian A Rosenberger, Marvin Thielert, Matthias Mann.
      
    DOI:  https://doi.org/10.1038/s41592-023-01771-9
  2. Sci Rep. 2023 Mar 07. 13(1): 3793
    Roles of PI3Kγ and PI3Kδ in mantle cell lymphoma proliferation and migration contributing to efficacy of the PI3Kγ/δ inhibitor duvelisib.
    Kathleen J Till, Mariah Abdullah, Tahera Alnassfan, Gallardo Zapata Janet, Thomas Marks, Silvia Coma, David T Weaver, Jonathan A Pachter, Andrew R Pettitt, Joseph R Slupsky.
      Mantle cell lymphoma (MCL) is an aggressive B-cell non-Hodgkin lymphoma that is incurable with existing therapies, and therefore presents a significant unmet clinical need. The ability of this disease to overcome therapy, including those that target the B cell receptor pathway which has a pathogenic role in MCL, highlights the need to develop new treatment strategies. Herein, we demonstrate that a distinguishing feature of lymph node resident MCL cells is the expression of phosphatidylinositol 3-kinase γ (PI3Kγ), a PI3K isoform that is not highly expressed in other B cells or B-cell malignancies. By exploring the role of PI3K in MCL using different PI3K isoform inhibitors, we provide evidence that duvelisib, a dual PI3Kδ/γ inhibitor, has a greater effect than PI3Kδ- and PI3Kγ-selective inhibitors in blocking the proliferation of primary MCL cells and MCL cell lines, and in inhibiting tumour growth in a mouse xenograft model. In addition, we demonstrated that PI3Kδ/γ signalling is critical for migration of primary MCL cells and cell lines. Our data indicates that aberrant expression of PI3Kγ is a critical feature of MCL pathogenesis. Thus, we suggest that the dual PI3Kδ/γ duvelisib would be effective for the treatment of mantle cell lymphoma.
    DOI:  https://doi.org/10.1038/s41598-023-30148-3
  3. Mol Biol Cell. 2023 Mar 08. mbcE22100476
    On the inference of ERK signaling dynamics from protein biosensor measurements.
    Shah Md Toufiqur Rahman, Jason M Haugh.
      The extracellular signal-regulated kinase (ERK) signaling pathway plays prominent roles in cell growth, proliferation, and differentiation. ERK signaling is dynamic, involving phosphorylation/dephosphorylation, nucleocytoplasmic shuttling, and interactions with scores of protein substrates in the cytosol and in the nucleus. Live-cell fluorescence microscopy using genetically encoded ERK biosensors offers the potential to infer those dynamics in individual cells. In this study, we have monitored ERK signaling using four commonly used translocation- and FRET-based biosensors in a common cell stimulation context. Consistent with previous reports, we found that each biosensor responds with unique kinetics; it is clear that there is not a single dynamic signature characterizing the complexity of ERK phosphorylation, translocation, and kinase activity. In particular, the widely adopted ERK Kinase Translocation Reporter (ERKKTR) gives a readout that reflects ERK activity in both compartments. Mathematical modeling offers an interpretation of the measured ERKKTR kinetics, in relation to cytosolic and nuclear ERK activity, and suggests that biosensor-specific dynamics substantially influence the measured output.
    DOI:  https://doi.org/10.1091/mbc.E22-10-0476
  4. Proc Natl Acad Sci U S A. 2023 Mar 14. 120(11): e2300605120
    Altered DNA repair pathway engagement by engineered CRISPR-Cas9 nucleases.
    Vikash P Chauhan, Phillip A Sharp, Robert Langer.
      CRISPR-Cas9 introduces targeted DNA breaks that engage competing DNA repair pathways, producing a spectrum of imprecise insertion/deletion mutations (indels) and precise templated mutations (precise edits). The relative frequencies of these pathways are thought to primarily depend on genomic sequence and cell state contexts, limiting control over mutational outcomes. Here, we report that engineered Cas9 nucleases that create different DNA break structures engage competing repair pathways at dramatically altered frequencies. We accordingly designed a Cas9 variant (vCas9) that produces breaks which suppress otherwise dominant nonhomologous end-joining (NHEJ) repair. Instead, breaks created by vCas9 are predominantly repaired by pathways utilizing homologous sequences, specifically microhomology-mediated end-joining (MMEJ) and homology-directed repair (HDR). Consequently, vCas9 enables efficient precise editing through HDR or MMEJ while suppressing indels caused by NHEJ in dividing and nondividing cells. These findings establish a paradigm of targeted nucleases custom-designed for specific mutational applications.
    Keywords:  CRISPR; DNA repair; genome editing; molecular engineering; precise editing
    DOI:  https://doi.org/10.1073/pnas.2300605120
  5. Life Sci Alliance. 2023 May;pii: e202201670. [Epub ahead of print]6(5):
    Analysis of context-specific KRAS-effector (sub)complexes in Caco-2 cells.
    Camille Ternet, Philipp Junk, Thomas Sevrin, Simona Catozzi, Erik Wåhlén, Johan Heldin, Giorgio Oliviero, Kieran Wynne, Christina Kiel.
      Ras is a key switch controlling cell behavior. In the GTP-bound form, Ras interacts with numerous effectors in a mutually exclusive manner, where individual Ras-effectors are likely part of larger cellular (sub)complexes. The molecular details of these (sub)complexes and their alteration in specific contexts are not understood. Focusing on KRAS, we performed affinity purification (AP)-mass spectrometry (MS) experiments of exogenously expressed FLAG-KRAS WT and three oncogenic mutants ("genetic contexts") in the human Caco-2 cell line, each exposed to 11 different culture media ("culture contexts") that mimic conditions relevant in the colon and colorectal cancer. We identified four effectors present in complex with KRAS in all genetic and growth contexts ("context-general effectors"). Seven effectors are found in KRAS complexes in only some contexts ("context-specific effectors"). Analyzing all interactors in complex with KRAS per condition, we find that the culture contexts had a larger impact on interaction rewiring than genetic contexts. We investigated how changes in the interactome impact functional outcomes and created a Shiny app for interactive visualization. We validated some of the functional differences in metabolism and proliferation. Finally, we used networks to evaluate how KRAS-effectors are involved in the modulation of functions by random walk analyses of effector-mediated (sub)complexes. Altogether, our work shows the impact of environmental contexts on network rewiring, which provides insights into tissue-specific signaling mechanisms. This may also explain why KRAS oncogenic mutants may be causing cancer only in specific tissues despite KRAS being expressed in most cells and tissues.
    DOI:  https://doi.org/10.26508/lsa.202201670
  6. Hum Genet. 2023 Mar 06.
    oFlowSeq: a quantitative approach to identify protein coding mutations affecting cell type enrichment using mosaic CRISPR-Cas9 edited cerebral organoids.
    Pepper Dawes, Liam F Murray, Meagan N Olson, Nathaniel J Barton, Molly Smullen, Madhusoodhanan Suresh, Guang Yan, Yucheng Zhang, Aria Fernandez-Fontaine, Jay English, Mohammed Uddin, ChangHui Pak, George M Church, Yingleong Chan, Elaine T Lim.
      Cerebral organoids are comprised of diverse cell types found in the developing human brain, and can be leveraged in the identification of critical cell types perturbed by genetic risk variants in common, neuropsychiatric disorders. There is great interest in developing high-throughput technologies to associate genetic variants with cell types. Here, we describe a high-throughput, quantitative approach (oFlowSeq) by utilizing CRISPR-Cas9, FACS sorting, and next-generation sequencing. Using oFlowSeq, we found that deleterious mutations in autism-associated gene KCTD13 resulted in increased proportions of Nestin+ cells and decreased proportions of TRA-1-60+ cells within mosaic cerebral organoids. We further identified that a locus-wide CRISPR-Cas9 survey of another 18 genes in the 16p11.2 locus resulted in most genes with > 2% maximum editing efficiencies for short and long indels, suggesting a high feasibility for an unbiased, locus-wide experiment using oFlowSeq. Our approach presents a novel method to identify genotype-to-cell type imbalances in an unbiased, high-throughput, quantitative manner.
    DOI:  https://doi.org/10.1007/s00439-023-02534-4
  7. Mol Cell Proteomics. 2023 Mar 07. pii: S1535-9476(23)00037-3. [Epub ahead of print] 100527
    Characterization of p38α signaling networks in cancer cells using quantitative proteomics and phosphoproteomics.
    Yuzhen Dan, Nevenka Radic, Marina Gay, Adrià Fernández-Torras, Gianluca Arauz, Marta Vilaseca, Patrick Aloy, Begoña Canovas, AngelR Nebreda.
      p38α (encoded by MAPK14) is a protein kinase that regulates cellular responses to almost all types of environmental and intracellular stresses. Upon activation, p38α phosphorylates many substrates both in the cytoplasm and nucleus, allowing this pathway to regulate a wide variety of cellular processes. While the role of p38α in the stress response has been widely investigated, its implication in cell homeostasis is less understood. To investigate the signaling networks regulated by p38α in proliferating cancer cells, we performed quantitative proteomic and phosphoproteomic analyses in breast cancer cells in which this pathway had been either genetically targeted or chemically inhibited. Our study identified with high confidence 35 proteins and 82 phosphoproteins (114 phosphosites) that are modulated by p38α, and highlighted the implication of various protein kinases, including MK2 and mTOR, in the p38α-regulated signaling networks. Moreover, functional analyses revealed an important contribution of p38α to the regulation of cell adhesion, DNA replication and RNA metabolism. Indeed, we provide experimental evidence supporting that p38α facilitates cancer cell adhesion, and showed that this p38α function is likely mediated by the modulation of the adaptor protein ArgBP2. Collectively, our results illustrate the complexity of the p38α regulated signaling networks, provide valuable information on p38α-dependent phosphorylation events in cancer cells, and document a mechanism by which p38α can regulate cell adhesion.
    Keywords:  cancer cell homeostasis; p38α; phosphoproteome; signal integration
    DOI:  https://doi.org/10.1016/j.mcpro.2023.100527
  8. Nat Methods. 2023 Mar;20(3): 339-346
    Sampling the proteome by emerging single-molecule and mass spectrometry methods.
    Michael J MacCoss, Javier Antonio Alfaro, Danielle A Faivre, Christine C Wu, Meni Wanunu, Nikolai Slavov.
      
    DOI:  https://doi.org/10.1038/s41592-023-01802-5
  9. Nat Methods. 2023 Mar;20(3): 317-318
    Single-cell proteomics: challenges and prospects.
      
    DOI:  https://doi.org/10.1038/s41592-023-01828-9
  10. Cells. 2023 Mar 06. pii: 812. [Epub ahead of print]12(5):
    Phosphorylation of LKB1 by PDK1 Inhibits Cell Proliferation and Organ Growth by Decreased Activation of AMPK.
    Sarah Borkowsky, Maximilian Gass, Azadeh Alavizargar, Johannes Hanewinkel, Ina Hallstein, Pavel Nedvetsky, Andreas Heuer, Michael P Krahn.
      The master kinase LKB1 is a key regulator of se veral cellular processes, including cell proliferation, cell polarity and cellular metabolism. It phosphorylates and activates several downstream kinases, including AMP-dependent kinase, AMPK. Activation of AMPK by low energy supply and phosphorylation of LKB1 results in an inhibition of mTOR, thus decreasing energy-consuming processes, in particular translation and, thus, cell growth. LKB1 itself is a constitutively active kinase, which is regulated by posttranslational modifications and direct binding to phospholipids of the plasma membrane. Here, we report that LKB1 binds to Phosphoinositide-dependent kinase (PDK1) by a conserved binding motif. Furthermore, a PDK1-consensus motif is located within the kinase domain of LKB1 and LKB1 gets phosphorylated by PDK1 in vitro. In Drosophila, knockin of phosphorylation-deficient LKB1 results in normal survival of the flies, but an increased activation of LKB1, whereas a phospho-mimetic LKB1 variant displays decreased AMPK activation. As a functional consequence, cell growth as well as organism size is decreased in phosphorylation-deficient LKB1. Molecular dynamics simulations of PDK1-mediated LKB1 phosphorylation revealed changes in the ATP binding pocket, suggesting a conformational change upon phosphorylation, which in turn can alter LKB1's kinase activity. Thus, phosphorylation of LKB1 by PDK1 results in an inhibition of LKB1, decreased activation of AMPK and enhanced cell growth.
    Keywords:  AMPK; LKB1; PDK1; cell proliferation; mTOR
    DOI:  https://doi.org/10.3390/cells12050812
  11. Nat Biotechnol. 2023 Mar 06.
    Microfluidics-free single-cell genomics with templated emulsification.
    Iain C Clark, Kristina M Fontanez, Robert H Meltzer, Yi Xue, Corey Hayford, Aaron May-Zhang, Chris D'Amato, Ahmad Osman, Jesse Q Zhang, Pabodha Hettige, Jacob S A Ishibashi, Cyrille L Delley, Daniel W Weisgerber, Joseph M Replogle, Marco Jost, Kiet T Phong, Vanessa E Kennedy, Cheryl A C Peretz, Esther A Kim, Siyou Song, William Karlon, Jonathan S Weissman, Catherine C Smith, Zev J Gartner, Adam R Abate.
      Current single-cell RNA-sequencing approaches have limitations that stem from the microfluidic devices or fluid handling steps required for sample processing. We develop a method that does not require specialized microfluidic devices, expertise or hardware. Our approach is based on particle-templated emulsification, which allows single-cell encapsulation and barcoding of cDNA in uniform droplet emulsions with only a vortexer. Particle-templated instant partition sequencing (PIP-seq) accommodates a wide range of emulsification formats, including microwell plates and large-volume conical tubes, enabling thousands of samples or millions of cells to be processed in minutes. We demonstrate that PIP-seq produces high-purity transcriptomes in mouse-human mixing studies, is compatible with multiomics measurements and can accurately characterize cell types in human breast tissue compared to a commercial microfluidic platform. Single-cell transcriptional profiling of mixed phenotype acute leukemia using PIP-seq reveals the emergence of heterogeneity within chemotherapy-resistant cell subsets that were hidden by standard immunophenotyping. PIP-seq is a simple, flexible and scalable next-generation workflow that extends single-cell sequencing to new applications.
    DOI:  https://doi.org/10.1038/s41587-023-01685-z
  12. Nat Commun. 2023 Mar 07. 14(1): 1201
    Non-canonical functions of SNAIL drive context-specific cancer progression.
    Mariel C Paul, Christian Schneeweis, Chiara Falcomatà, Chuan Shan, Daniel Rossmeisl, Stella Koutsouli, Christine Klement, Magdalena Zukowska, Sebastian A Widholz, Moritz Jesinghaus, Konstanze K Heuermann, Thomas Engleitner, Barbara Seidler, Katia Sleiman, Katja Steiger, Markus Tschurtschenthaler, Benjamin Walter, Sören A Weidemann, Regina Pietsch, Angelika Schnieke, Roland M Schmid, Maria S Robles, Geoffroy Andrieux, Melanie Boerries, Roland Rad, Günter Schneider, Dieter Saur.
      SNAIL is a key transcriptional regulator in embryonic development and cancer. Its effects in physiology and disease are believed to be linked to its role as a master regulator of epithelial-to-mesenchymal transition (EMT). Here, we report EMT-independent oncogenic SNAIL functions in cancer. Using genetic models, we systematically interrogated SNAIL effects in various oncogenic backgrounds and tissue types. SNAIL-related phenotypes displayed remarkable tissue- and genetic context-dependencies, ranging from protective effects as observed in KRAS- or WNT-driven intestinal cancers, to dramatic acceleration of tumorigenesis, as shown in KRAS-induced pancreatic cancer. Unexpectedly, SNAIL-driven oncogenesis was not associated with E-cadherin downregulation or induction of an overt EMT program. Instead, we show that SNAIL induces bypass of senescence and cell cycle progression through p16INK4A-independent inactivation of the Retinoblastoma (RB)-restriction checkpoint. Collectively, our work identifies non-canonical EMT-independent functions of SNAIL and unravel its complex context-dependent role in cancer.
    DOI:  https://doi.org/10.1038/s41467-023-36505-0
  13. J Cell Commun Signal. 2023 Mar 07.
    Temporal phosphoproteomic analysis of VEGF-A signaling in HUVECs: an insight into early signaling events associated with angiogenesis.
    Chandran S Abhinand, Josephine Galipon, Masaru Mori, Poornima Ramesh, Thottethodi Subrahmanya Keshava Prasad, Rajesh Raju, Perumana R Sudhakaran, Masaru Tomita.
      Vascular endothelial growth factor-A (VEGF-A) is one of the primary factors promoting angiogenesis in endothelial cells. Although defects in VEGF-A signaling are linked to diverse pathophysiological conditions, the early phosphorylation-dependent signaling events pertinent to VEGF-A signaling remain poorly defined. Hence, a temporal quantitative phosphoproteomic analysis was performed in human umbilical vein endothelial cells (HUVECs) treated with VEGF-A-165 for 1, 5 and 10 min. This led to the identification and quantification of 1971 unique phosphopeptides corresponding to 961 phosphoproteins and 2771 phosphorylation sites in total. Specifically, 69, 153, and 133 phosphopeptides corresponding to 62, 125, and 110 phosphoproteins respectively, were temporally phosphorylated at 1, 5, and 10 min upon addition of VEGF-A. These phosphopeptides included 14 kinases, among others. This study also captured the phosphosignaling events directed through RAC, FAK, PI3K-AKT-MTOR, ERK, and P38 MAPK modules with reference to our previously assembled VEGF-A/VEGFR2 signaling pathway map in HUVECs. Apart from a significant enrichment of biological processes such as cytoskeleton organization and actin filament binding, our results also suggest a role of AAK1-AP2M1 in the regulation of VEGFR endocytosis. Taken together, the temporal quantitative phosphoproteomics analysis of VEGF signaling in HUVECs revealed early signaling events and we believe that this analysis will serve as a starting point for the analysis of differential signaling across VEGF members toward the full elucidation of their role in the angiogenesis processes. Workflow for the identification of early phosphorylation events induced by VEGF-A-165 in HUVEC cells.
    Keywords:  Angiogenesis; Cytoskeleton organization; HUVEC; Phosphoproteomics; VEGF-A
    DOI:  https://doi.org/10.1007/s12079-023-00736-z
  14. Nat Chem Biol. 2023 Mar 09.
    Sniper2L is a high-fidelity Cas9 variant with high activity.
    Young-Hoon Kim, Nahye Kim, Ikenna Okafor, Sungchul Choi, Seonwoo Min, Joonsun Lee, Seung-Min Bae, Keunwoo Choi, Janice Choi, Vinayak Harihar, Youngho Kim, Jin-Soo Kim, Benjamin P Kleinstiver, Jungjoon K Lee, Taekjip Ha, Hyongbum Henry Kim.
      Although several high-fidelity SpCas9 variants have been reported, it has been observed that this increased specificity is associated with reduced on-target activity, limiting the applications of the high-fidelity variants when efficient genome editing is required. Here, we developed an improved version of Sniper-Cas9, Sniper2L, which represents an exception to this trade-off trend as it showed higher specificity with retained high activity. We evaluated Sniper2L activities at a large number of target sequences and developed DeepSniper, a deep learning model that can predict the activity of Sniper2L. We also confirmed that Sniper2L can induce highly efficient and specific editing at a large number of target sequences when it is delivered as a ribonucleoprotein complex. Mechanically, the high specificity of Sniper2L originates from its superior ability to avoid unwinding a target DNA containing even a single mismatch. We envision that Sniper2L will be useful when efficient and specific genome editing is required.
    DOI:  https://doi.org/10.1038/s41589-023-01279-5
  15. Nat Methods. 2023 Mar 06.
    We need a plan D.
    Richard Sever.
      
    DOI:  https://doi.org/10.1038/s41592-023-01817-y
  16. Anal Chem. 2023 Mar 10.
    Mass Spectrometry Imaging Reveals Early Metabolic Priming of Cell Lineage in Differentiating Human-Induced Pluripotent Stem Cells.
    Arina A Nikitina, Alexandria Van Grouw, Tanya Roysam, Danning Huang, Facundo M Fernández, Melissa L Kemp.
      Induced pluripotent stem cells (iPSCs) hold great promise in regenerative medicine; however, few algorithms of quality control at the earliest stages of differentiation have been established. Despite lipids having known functions in cell signaling, their role in pluripotency maintenance and lineage specification is underexplored. We investigated the changes in iPSC lipid profiles during the initial loss of pluripotency over the course of spontaneous differentiation using the co-registration of confocal microscopy and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging. We identified phosphatidylethanolamine (PE) and phosphatidylinositol (PI) species that are highly informative of the temporal stage of differentiation and can reveal iPS cell lineage bifurcation occurring metabolically. Several PI species emerged from the machine learning analysis of MS data as the early metabolic markers of pluripotency loss, preceding changes in the pluripotency transcription factor Oct4. The manipulation of phospholipids via PI 3-kinase inhibition during differentiation manifested in the spatial reorganization of the iPS cell colony and elevated expression of NCAM-1. In addition, the continuous inhibition of phosphatidylethanolamine N-methyltransferase during differentiation resulted in the enhanced maintenance of pluripotency. Our machine learning analysis highlights the predictive power of lipidomic metrics for evaluating the early lineage specification in the initial stages of spontaneous iPSC differentiation.
    DOI:  https://doi.org/10.1021/acs.analchem.2c04416
  17. Science. 2023 Mar 10. 379(6636): 996-1003
    Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase.
    Kevin G Hicks, Ahmad A Cluntun, Heidi L Schubert, Sean R Hackett, Jordan A Berg, Paul G Leonard, Mariana A Ajalla Aleixo, Youjia Zhou, Alex J Bott, Sonia R Salvatore, Fei Chang, Aubrie Blevins, Paige Barta, Samantha Tilley, Aaron Leifer, Andrea Guzman, Ajak Arok, Sarah Fogarty, Jacob M Winter, Hee-Chul Ahn, Karen N Allen, Samuel Block, Iara A Cardoso, Jianping Ding, Ingrid Dreveny, William C Gasper, Quinn Ho, Atsushi Matsuura, Michael J Palladino, Sabin Prajapati, Pengkai Sun, Kai Tittmann, Dean R Tolan, Judith Unterlass, Andrew P VanDemark, Matthew G Vander Heiden, Bradley A Webb, Cai-Hong Yun, Pengkai Zhao, Bei Wang, Francisco J Schopfer, Christopher P Hill, Maria Cristina Nonato, Florian L Muller, James E Cox, Jared Rutter.
      Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.
    DOI:  https://doi.org/10.1126/science.abm3452
  18. Nat Chem Biol. 2023 Mar 06.
    A chemically controlled Cas9 switch enables temporal modulation of diverse effectors.
    Cindy T Wei, Nicholas A Popp, Omri Peleg, Rachel L Powell, Elhanan Borenstein, Dustin J Maly, Douglas M Fowler.
      CRISPR-Cas9 has yielded a plethora of effectors, including targeted transcriptional activators, base editors and prime editors. Current approaches for inducibly modulating Cas9 activity lack temporal precision and require extensive screening and optimization. We describe a versatile, chemically controlled and rapidly activated single-component DNA-binding Cas9 switch, ciCas9, which we use to confer temporal control over seven Cas9 effectors, including two cytidine base editors, two adenine base editors, a dual base editor, a prime editor and a transcriptional activator. Using these temporally controlled effectors, we analyze base editing kinetics, showing that editing occurs within hours and that rapid early editing of nucleotides predicts eventual editing magnitude. We also reveal that editing at preferred nucleotides within target sites increases the frequency of bystander edits. Thus, the ciCas9 switch offers a simple, versatile approach to generating chemically controlled Cas9 effectors, informing future effector engineering and enabling precise temporal effector control for kinetic studies.
    DOI:  https://doi.org/10.1038/s41589-023-01278-6
  19. Nat Methods. 2023 Mar;20(3): 336-338
    Not if but when nanopore protein sequencing meets single-cell proteomics.
    Keisuke Motone, Jeff Nivala.
      
    DOI:  https://doi.org/10.1038/s41592-023-01800-7
  20. Am J Physiol Cell Physiol. 2023 Mar 06.
    Physiologically relevant culture medium Plasmax improves human placental trophoblast stem cell function.
    Giulia Avellino, Ruhi Deshmukh, Stephanie N Rogers, D Stephen Charnock-Jones, Gordon C S Smith, Saverio Tardito, Irving L M H Aye.
      Human trophoblast cultures provide powerful tools to model key processes of placental development. In vitro trophoblast studies to date have relied on commercial media which contains non-physiological levels of nutrients, and the impact of these conditions on trophoblast metabolism and function is unknown. Here we show that the physiological medium (Plasmaxä) with nutrient and metabolite concentrations recapitulating human plasma improves human trophoblast stem cell (hTSC) proliferation and differentiation compared to standard medium (DMEM-F12). hTSCs cultured in Plasmax-based medium also show altered glycolytic and mitochondrial metabolism, as well as reduced S-adenosylmethionine/S-adenosyl-homosysteine ratio compared to DMEM-F12-based medium. These findings demonstrate the importance of the nutritional environment for phenotyping cultured human trophoblasts.
    Keywords:  culture medium; placenta; stem cells
    DOI:  https://doi.org/10.1152/ajpcell.00581.2022
  21. Nat Methods. 2023 Mar;20(3): 331-335
    Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput.
    James Eberwine, Junhyong Kim, Ron C Anafi, Steven Brem, Maja Bucan, Stephen A Fisher, M Sean Grady, Amy E Herr, David Issadore, Hyejoong Jeong, HyunBum Kim, Daeyeon Lee, Stanislav Rubakhin, Jai-Yoon Sul, Jonathan V Sweedler, John A Wolf, Kenneth S Zaret, James Zou.
      
    DOI:  https://doi.org/10.1038/s41592-023-01788-0
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