bims-pideca 2023-01-08 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2023–01–08
eightteen papers selected by
Ralitsa Radostinova Madsen, University College London

Genetic heterogeneity and tissue-specific patterns of tumors with multiple PIK3CA mutations.
Unique ligand and kinase-independent roles of the insulin receptor in regulation of cell cycle, senescence and apoptosis.
Activated PI3Kδ syndrome 1 mimicking systemic lupus erythematosus and secondary Sjögren's syndrome-like phenotype without recurrent infections: A case report.
Exploiting multivalency and cooperativity of gold nanoparticles for binding phosphatidylinositol (3,4,5)-trisphosphate at sub-nanomolar concentrations.
Enhanced protein acetylation initiates fatty acid-mediated inhibition of cardiac glucose transport.
Dynamic regulation of RAS and RAS signaling.
Whole-genome CRISPR screening identifies PI3K/AKT as a downstream component of the oncogenic GNAQ-Focal Adhesion Kinase signaling circuitry.
Feedback in the β-catenin destruction complex imparts bistability and cellular memory.
Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.
STAT proteins in cancer: orchestration of metabolism.
Determining On-Target, Off-Target, and Copy Number Status of Transgenic Events After CRISPR/Cas9 Targeted AAVS1 Safe-Harbor Modification of iPSCs Using Double-Control Quantitative Copy Number PCR.
Generation and immunofluorescent validation of gene knockouts in adult human colonic organoids using multi-guide RNA CRISPR-Cas9.
Metabolic regulation of species-specific developmental rates.
Changing the culture for the future: time to take brain drain in academics seriously.
Precise cut-and-paste DNA insertion using engineered type V-K CRISPR-associated transposases.
A culture platform to study quiescent hematopoietic stem cells following genome editing.
Hallmarks of aging: An expanding universe.
Dynamic metabolome profiling uncovers potential TOR signaling genes.

Clin Cancer Res. 2023 Jan 03. pii: CCR-22-2270. [Epub ahead of print]

Genetic heterogeneity and tissue-specific patterns of tumors with multiple PIK3CA mutations.

Smruthy Sivakumar, Dexter X Jin, Ruchita Rathod, Jeffrey Ross, Lewis C Cantley, Maurizio Scaltriti, Jessica W Chen, Katherine E Hutchinson, Timothy R Wilson, Ethan S Sokol, Neil Vasan.

PURPOSE: To comprehensively characterize tissue-specific and molecular subclasses of multiple PIK3CA (multi-PIK3CA) mutations and assess their impact on potential therapeutic outcomes.
EXPERIMENTAL DESIGN: We profiled a pan-cancer cohort comprised of 352,392 samples across 66 tumor types using a targeted hybrid capture-based next generation sequencing panel covering at least 324 cancer-related genes. Molecularly defined subgroups, allelic configuration, clonality, and mutational signatures were identified and tested for association with PI3K inhibitor therapeutic response.
RESULTS: Multi-PIK3CA mutations are found in 11% of all PIK3CA-mutant tumors, including 9% of low tumor mutational burden PIK3CA-mutant tumors, and are enriched in breast and gynecologic cancers. Multi-PIK3CA mutations are frequently clonal and in cis on the same allele and occur at characteristic positions across tumor types. These mutations tend to be mutually exclusive of mutations in other driver genes, and of genes in the PI3K pathway. Among PIK3CA-mutant tumors with a high TMB, 18% are multi-PIK3CA mutant and often harbor an APOBEC mutational signature. Despite large differences in specific allele combinations comprising multi-PIK3CA mutant tumors, especially across cancer types, patients with different classes of multi-PIK3CA mutant ER+ HER2- breast cancers respond similarly to PI3K inhibition.
CONCLUSIONS: Our pan-tumor study provides biological insights into the genetic heterogeneity and tissue specificities of multi-PIK3CA mutations, with potential clinical utility to guide PI3K inhibition strategies.

DOI: https://doi.org/10.1158/1078-0432.CCR-22-2270
Nat Commun. 2023 Jan 04. 14(1): 57

Unique ligand and kinase-independent roles of the insulin receptor in regulation of cell cycle, senescence and apoptosis.

Hirofumi Nagao, Ashok Kumar Jayavelu, Weikang Cai, Hui Pan, Jonathan M Dreyfuss, Thiago M Batista, Bruna B Brandão, Matthias Mann, C Ronald Kahn.

Insulin acts through the insulin receptor (IR) tyrosine kinase to exert its classical metabolic and mitogenic actions. Here, using receptors with either short or long deletion of the β-subunit or mutation of the kinase active site (K1030R), we have uncovered a second, previously unrecognized IR signaling pathway that is intracellular domain-dependent, but ligand and tyrosine kinase-independent (LYK-I). These LYK-I actions of the IR are linked to changes in phosphorylation of a network of proteins involved in the regulation of extracellular matrix organization, cell cycle, ATM signaling and cellular senescence; and result in upregulation of expression of multiple extracellular matrix-related genes and proteins, down-regulation of immune/interferon-related genes and proteins, and increased sensitivity to apoptosis. Thus, in addition to classical ligand and tyrosine kinase-dependent (LYK-D) signaling, the IR regulates a second, ligand and tyrosine kinase-independent (LYK-I) pathway, which regulates the cellular machinery involved in senescence, matrix interaction and response to extrinsic challenges.

DOI: https://doi.org/10.1038/s41467-022-35693-5
Front Pediatr. 2022 ;10 1077324

Activated PI3Kδ syndrome 1 mimicking systemic lupus erythematosus and secondary Sjögren's syndrome-like phenotype without recurrent infections: A case report.

Jing Yin, Jijun Ma, Jingyue Xia, Yang Cao, Chongwei Li.

  Activated phosphoinositide 3-kinase-δ syndrome 1 (APDS1) is a combined immunodeficiency caused by a heterozygous gain-of-function mutation in PIK3CD, encoding the p110δ catalytic subunit of phosphoinositide 3-kinase δ (PI3Kδ). APDS1 is characterized by recurrent sinopulmonary infections, leading to airway damage, chronic herpes viremia, lymphoproliferation, and autoimmune and inflammatory diseases. Several cases of systemic lupus erythematosus (SLE) have been reported in APDS1; however, Sjögren's syndrome (SS) or an SS-like phenotype is rarely described in patients with APDS1. In this study, we report a 4-year-old girl with APDS1 who did not experience recurrent sinopulmonary infections and chronic viremia but presented with cytopenia, proteinuria, hypocomplementemia, and positive antinuclear antibodies that met the classification criteria for SLE. Additionally, the patient also mimicked a secondary SS-like phenotype based on recurrent parotitis and labial salivary gland biopsy. The patient achieved remission after treatment with sirolimus and immunosuppressive therapy. This case report enriches the clinical phenotype of APDS1 and provides a reference for the diagnosis and therapy of patients with APDS1.

Keywords:  PIK3CD; Sjögren's syndrome; activated phosphoinositide 3-kinase-δ syndrome; autoimmune; p110δ; systemic lupus erythematosus

DOI:  https://doi.org/10.3389/fped.2022.1077324
Org Biomol Chem. 2023 Jan 05.

Exploiting multivalency and cooperativity of gold nanoparticles for binding phosphatidylinositol (3,4,5)-trisphosphate at sub-nanomolar concentrations.

Flavio Della Sala, Elisa Ceresara, Fabrizio Micheli, Stefano Fontana, Leonard J Prins, Paolo Scrimin.

Cationic, monolayer-protected gold nanoparticles provide a multivalent charged surface and a hydrophobic monolayer that synergistically contribute to the binding of phosphatidylinositol (3,4,5)-trisphosphate, a relevant biomarker. The observed dissociation constant is in the picomolar region, providing the possibility of using these gold nanoparticles for the selective extraction of this molecule from biological fluids.

DOI: https://doi.org/10.1039/d2ob02088b
Am J Physiol Heart Circ Physiol. 2023 Jan 06.

Enhanced protein acetylation initiates fatty acid-mediated inhibition of cardiac glucose transport.

Marine De Loof, Edith Renguet, Audrey Ginion, Caroline Bouzin, Sandrine Horman, Christophe Beauloye, Luc Bertrand, Laurent Bultot.

  Fatty acids (FAs) rapidly and efficiently reduce cardiac glucose uptake in the Randle cycle or glucose-FA cycle. This fine-tuned physiological regulation is critical to allow optimal substrate allocation during fasted and fed states. However, the mechanisms involved in the direct FA-mediated control of glucose transport have not been totally elucidated yet. We previously reported that leucine and ketone bodies, other cardiac substrates, impair glucose uptake by increasing global protein acetylation from acetyl-CoA. As FAs generate acetyl-CoA as well, we postulated that protein acetylation is enhanced by FAs and participates to their inhibitory action on cardiac glucose uptake. Here, we demonstrated that both palmitate and oleate promoted a rapid increase in protein acetylation in primary cultured adult rat cardiomyocytes, which correlated with an inhibition of insulin-stimulated glucose uptake. This glucose absorption deficit was caused by an impairment in the translocation of vesicles containing the glucose transporter GLUT4 to the plasma membrane, although insulin signaling remained unaffected. Interestingly, pharmacological inhibition of lysine acetyltransferases (KATs) prevented this increase in protein acetylation and glucose uptake inhibition induced by FAs. Similarly, FA-mediated inhibition of insulin-stimulated glucose uptake could be prevented by KAT inhibitors in perfused hearts. To summarize, enhanced protein acetylation can be considered as an early event in the FA-induced inhibition of glucose transport in the heart, explaining part of the Randle cycle.

Keywords:  Acetylation; Fatty acids; Glucose uptake; Insulin; Randle cycle

DOI:  https://doi.org/10.1152/ajpheart.00449.2022
Biochem J. 2023 Jan 13. 480(1): 1-23

Dynamic regulation of RAS and RAS signaling.

Walter Kolch, Dénes Berta, Edina Rosta.

  RAS proteins regulate most aspects of cellular physiology. They are mutated in 30% of human cancers and 4% of developmental disorders termed Rasopathies. They cycle between active GTP-bound and inactive GDP-bound states. When active, they can interact with a wide range of effectors that control fundamental biochemical and biological processes. Emerging evidence suggests that RAS proteins are not simple on/off switches but sophisticated information processing devices that compute cell fate decisions by integrating external and internal cues. A critical component of this compute function is the dynamic regulation of RAS activation and downstream signaling that allows RAS to produce a rich and nuanced spectrum of biological outputs. We discuss recent findings how the dynamics of RAS and its downstream signaling is regulated. Starting from the structural and biochemical properties of wild-type and mutant RAS proteins and their activation cycle, we examine higher molecular assemblies, effector interactions and downstream signaling outputs, all under the aspect of dynamic regulation. We also consider how computational and mathematical modeling approaches contribute to analyze and understand the pleiotropic functions of RAS in health and disease.

Keywords:  RAS proteins; biological networks; cancer; dynamics; signaling

DOI:  https://doi.org/10.1042/BCJ20220234
J Biol Chem. 2022 Dec 31. pii: S0021-9258(22)01309-6. [Epub ahead of print] 102866

Whole-genome CRISPR screening identifies PI3K/AKT as a downstream component of the oncogenic GNAQ-Focal Adhesion Kinase signaling circuitry.

Nadia Arang, Simone Lubrano, Damiano Cosimo Rigiracciolo, Daniela Nachmanson, Scott M Lippman, Prashant Mali, Olivier Harismendy, J Silvio Gutkind.

G proteins and G protein-coupled receptors (GPCRs) activate a diverse array of signal transduction pathways that promote cell growth and survival. Indeed, hotspot activating mutations in GNAQ/GNA11, encoding Gαq proteins, are known to be driver oncogenes in uveal melanoma (UM), for which there are limited effective therapies currently available. Focal Adhesion Kinase (FAK) has been recently shown to be a central mediator of Gαq-driven signaling in UM, and as a result, is being explored clinically as a therapeutic target for UM, both alone and in combination therapies. Despite this, the repertoire of Gαq/FAK-regulated signaling mechanisms have not been fully elucidated. Here, we used a whole-genome CRISPR screen in GNAQ-mutant UM cells to identify mechanisms that, when overactivated, lead to reduced sensitivity to FAK inhibition. In this way, we found the PI3K/AKT signaling pathway represented a major resistance driver. Our dissection of the underlying mechanisms revealed that Gαq promotes PI3K/AKT activation via a conserved signaling circuitry mediated by FAK. Further analysis demonstrated that FAK activates PI3K through the association and tyrosine phosphorylation of the p85 regulatory subunit of PI3K, and that UM cells require PI3K/AKT signaling for survival. These findings establish a novel link between Gαq-driven signaling and the stimulation of PI3K, as well as demonstrate aberrant activation of signaling networks underlying the growth and survival of UM and other Gαq-driven malignancies.

DOI: https://doi.org/10.1016/j.jbc.2022.102866
Proc Natl Acad Sci U S A. 2023 Jan 10. 120(2): e2208787120

Feedback in the β-catenin destruction complex imparts bistability and cellular memory.

Mary Jo Cantoria, Elaheh Alizadeh, Janani Ravi, Reeba P Varghese, Nawat Bunnag, Kelvin W Pond, Arminja N Kettenbach, Yashi Ahmed, Andrew L Paek, John J Tyson, Konstantin Doubrovinski, Ethan Lee, Curtis A Thorne.

  Wnt ligands are considered classical morphogens, for which the strength of the cellular response is proportional to the concentration of the ligand. Herein, we show an emergent property of bistability arising from feedback among the Wnt destruction complex proteins that target the key transcriptional co-activator β-catenin for degradation. Using biochemical reconstitution, we identified positive feedback between the scaffold protein Axin and the kinase glycogen synthase kinase 3 (GSK3). Theoretical modeling of this feedback between Axin and GSK3 suggested that the activity of the destruction complex exhibits bistable behavior. We experimentally confirmed these predictions by demonstrating that cellular cytoplasmic β-catenin concentrations exhibit an "all-or-none" response with sustained memory (hysteresis) of the signaling input. This bistable behavior was transformed into a graded response and memory was lost through inhibition of GSK3. These findings provide a mechanism for establishing decisive, switch-like cellular response and memory upon Wnt pathway stimulation.

Keywords:  Wnt signaling; bistability; signal transduction

DOI:  https://doi.org/10.1073/pnas.2208787120
Nat Biotechnol. 2023 Jan 02.

Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.

IMI DIRECT Consortium

The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature of multi-modal data makes integration and inference a non-trivial task. We developed a deep-learning-based framework, multi-omics variational autoencoders (MOVE), to integrate such data and applied it to a cohort of 789 people with newly diagnosed type 2 diabetes with deep multi-omics phenotyping from the DIRECT consortium. Using in silico perturbations, we identified drug-omics associations across the multi-modal datasets for the 20 most prevalent drugs given to people with type 2 diabetes with substantially higher sensitivity than univariate statistical tests. From these, we among others, identified novel associations between metformin and the gut microbiota as well as opposite molecular responses for the two statins, simvastatin and atorvastatin. We used the associations to quantify drug-drug similarities, assess the degree of polypharmacy and conclude that drug effects are distributed across the multi-omics modalities.

DOI: https://doi.org/10.1038/s41587-022-01520-x
Nat Rev Cancer. 2023 Jan 03.

STAT proteins in cancer: orchestration of metabolism.

Yi-Jia Li, Chunyan Zhang, Antons Martincuks, Andreas Herrmann, Hua Yu.

Reprogrammed metabolism is a hallmark of cancer. However, the metabolic dependency of cancer, from tumour initiation through disease progression and therapy resistance, requires a spectrum of distinct reprogrammed cellular metabolic pathways. These pathways include aerobic glycolysis, oxidative phosphorylation, reactive oxygen species generation, de novo lipid synthesis, fatty acid β-oxidation, amino acid (notably glutamine) metabolism and mitochondrial metabolism. This Review highlights the central roles of signal transducer and activator of transcription (STAT) proteins, notably STAT3, STAT5, STAT6 and STAT1, in orchestrating the highly dynamic metabolism not only of cancer cells but also of immune cells and adipocytes in the tumour microenvironment. STAT proteins are able to shape distinct metabolic processes that regulate tumour progression and therapy resistance by transducing signals from metabolites, cytokines, growth factors and their receptors; defining genetic programmes that regulate a wide range of molecules involved in orchestration of metabolism in cancer and immune cells; and regulating mitochondrial activity at multiple levels, including energy metabolism and lipid-mediated mitochondrial integrity. Given the central role of STAT proteins in regulation of metabolic states, they are potential therapeutic targets for altering metabolic reprogramming in cancer.

DOI: https://doi.org/10.1038/s41568-022-00537-3
Curr Protoc. 2023 Jan;3(1): e635

Determining On-Target, Off-Target, and Copy Number Status of Transgenic Events After CRISPR/Cas9 Targeted AAVS1 Safe-Harbor Modification of iPSCs Using Double-Control Quantitative Copy Number PCR.

Brit-Maren Michaud Schjeide, Gerhard Paul Püschel.

  Double-control quantitative copy number PCR (dc-qcnPCR) is a recently described tool that can be used to quantify donor DNA insertions in genetically modified monoclonal cell lines. In conjunction with an insert-confirmation PCR, the technique can quickly and easily identify clones containing on-target heterozygous or homozygous donor DNA integrations and exclude off-target insertions. The genetic manipulation of immortal cell lines is a versatile tool to elucidate cellular signaling pathways and protein functions. Despite recent advances in the precision of genetic engineering tools such as CRISPR/Cas9, transcription-activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs), it is still essential to verify the accurate insertion of the sequence of interest (donor DNA) into the targeted genomic DNA (gDNA) locus. This precise integration into a genetic safe harbor, and exclusion of the donor DNA from functionally relevant genes, can ensure normal cellular functionality. Current methods to analyze the specificity of donor DNA insertions either are cost-prohibitive or create dependency on manufacturers for assay design and production. The dc-qcnPCR method is a simple, yet powerful, approach that can be prepared and carried out in any laboratory equipped with standard molecular biology supplies. Here we provide step-by-step instructions to prepare and perform the dc-qcnPCR, and its companion insert-confirmation PCR, to determine donor DNA insertion numbers in monoclonal cell lines genetically modified through CRISPR/Cas9. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Genetic modification at AAVS1 safe harbor in induced pluripotent stem cells (IMR90-4) using CRISPR/Cas9: from plasmid design to monoclonal expansion Support Protocol 1: Measurement of Gaussia luciferase activity to verify reporter protein functionality Support Protocol 2: Verification of monoclonal expansion using immunofluorescence. Basic Protocol 2: Insert-confirmation PCR Basic Protocol 3: Design and preparation of double-control quantitative copy number PCR reagents and quantification of donor DNA integrations in genetically modified monoclonal cells.

Keywords:  AAVS1 safe harbor; CRISPR/Cas9; iPSC; off-target; on-target; quantification; transgene

DOI:  https://doi.org/10.1002/cpz1.635
STAR Protoc. 2023 Jan 03. pii: S2666-1667(22)00858-9. [Epub ahead of print]4(1): 101978

Generation and immunofluorescent validation of gene knockouts in adult human colonic organoids using multi-guide RNA CRISPR-Cas9.

Dedrick Kok Hong Chan, Scott David Collins, Simon James Alexander Buczacki.

  While readily achieved in cell lines, the application of CRISPR-Cas9 gene editing in human-derived organoids suffers from limited efficacy and complex protocols. Here, we describe a multi-guide RNA CRISPR-Cas9 gene-editing protocol which efficiently achieves complete gene knockout in adult human colonic organoids. This protocol also describes crucial steps including how to harvest patient tissue to maximize gene-editing efficacy and a technique to validate gene knockout following editing with immunofluorescent staining of the organoids against the target protein.

Keywords:  CRISPR; Microscopy; Organoids

DOI:  https://doi.org/10.1016/j.xpro.2022.101978
Nature. 2023 Jan 04.

Metabolic regulation of species-specific developmental rates.

Margarete Diaz-Cuadros, Teemu P Miettinen, Owen S Skinner, Dylan Sheedy, Carlos Manlio Díaz-García, Svetlana Gapon, Alexis Hubaud, Gary Yellen, Scott R Manalis, William M Oldham, Olivier Pourquié.

Animals display substantial inter-species variation in the rate of embryonic development despite a broad conservation of the overall sequence of developmental events. Differences in biochemical reaction rates, including the rates of protein production and degradation, are thought to be responsible for species-specific rates of development1-3. However, the cause of differential biochemical reaction rates between species remains unknown. Here, using pluripotent stem cells, we have established an in vitro system that recapitulates the twofold difference in developmental rate between mouse and human embryos. This system provides a quantitative measure of developmental speed as revealed by the period of the segmentation clock, a molecular oscillator associated with the rhythmic production of vertebral precursors. Using this system, we show that mass-specific metabolic rates scale with the developmental rate and are therefore higher in mouse cells than in human cells. Reducing these metabolic rates by inhibiting the electron transport chain slowed down the segmentation clock by impairing the cellular NAD+/NADH redox balance and, further downstream, lowering the global rate of protein synthesis. Conversely, increasing the NAD+/NADH ratio in human cells by overexpression of the Lactobacillus brevis NADH oxidase LbNOX increased the translation rate and accelerated the segmentation clock. These findings represent a starting point for the manipulation of developmental rate, with multiple translational applications including accelerating the differentiation of human pluripotent stem cells for disease modelling and cell-based therapies.

DOI: https://doi.org/10.1038/s41586-022-05574-4
Trends Cell Biol. 2022 Dec 31. pii: S0962-8924(22)00276-8. [Epub ahead of print]

Changing the culture for the future: time to take brain drain in academics seriously.

Chi-Ping Day, Kerrie L Marie, Ashani Weeraratna.

DOI: https://doi.org/10.1016/j.tcb.2022.12.002
Nat Biotechnol. 2023 Jan 02.

Precise cut-and-paste DNA insertion using engineered type V-K CRISPR-associated transposases.

Connor J Tou, Benno Orr, Benjamin P Kleinstiver.

CRISPR-associated transposases (CASTs) enable recombination-independent, multi-kilobase DNA insertions at RNA-programmed genomic locations. However, the utility of type V-K CASTs is hindered by high off-target integration and a transposition mechanism that results in a mixture of desired simple cargo insertions and undesired plasmid cointegrate products. Here we overcome both limitations by engineering new CASTs with improved integration product purity and genome-wide specificity. To do so, we engineered a nicking homing endonuclease fusion to TnsB (named HELIX) to restore the 5' nicking capability needed for cargo excision on the DNA donor. HELIX enables cut-and-paste DNA insertion with up to 99.4% simple insertion product purity, while retaining robust integration efficiencies on genomic targets. HELIX has substantially higher on-target specificity than canonical CASTs, and we identify several novel factors that further regulate targeted and genome-wide integration. Finally, we extend HELIX to other type V-K orthologs and demonstrate the feasibility of HELIX-mediated integration in human cell contexts.

DOI: https://doi.org/10.1038/s41587-022-01574-x
Cell Rep Methods. 2022 Dec 19. 2(12): 100354

A culture platform to study quiescent hematopoietic stem cells following genome editing.

Kohei Shiroshita, Hiroshi Kobayashi, Shintaro Watanuki, Daiki Karigane, Yuriko Sorimachi, Shinya Fujita, Shinpei Tamaki, Miho Haraguchi, Naoki Itokawa, Kazumasa Aoyoama, Shuhei Koide, Yosuke Masamoto, Kenta Kobayashi, Ayako Nakamura-Ishizu, Mineo Kurokawa, Atsushi Iwama, Shinichiro Okamoto, Keisuke Kataoka, Keiyo Takubo.

  Other than genetically engineered mice, few reliable platforms are available for the study of hematopoietic stem cell (HSC) quiescence. Here we present a platform to analyze HSC cell cycle quiescence by combining culture conditions that maintain quiescence with a CRISPR-Cas9 genome editing system optimized for HSCs. We demonstrate that preculture of HSCs enhances editing efficiency by facilitating nuclear transport of ribonucleoprotein complexes. For post-editing culture, mouse and human HSCs edited based on non-homologous end joining and cultured under low-cytokine, low-oxygen, and high-albumin conditions retain their phenotypes and quiescence better than those cultured under the proliferative conditions. Using this approach, HSCs regain quiescence even after editing by homology-directed repair. Our results show that low-cytokine culture conditions for gene-edited HSCs are a useful approach for investigating HSC quiescence ex vivo.

Keywords:  CRISPR-Cas9; genome editing; hematopoietic stem cell; quiescence; stem cell culture

DOI:  https://doi.org/10.1016/j.crmeth.2022.100354
Cell. 2022 Dec 26. pii: S0092-8674(22)01377-0. [Epub ahead of print]

Hallmarks of aging: An expanding universe.

Carlos López-Otín, Maria A Blasco, Linda Partridge, Manuel Serrano, Guido Kroemer.

Aging is driven by hallmarks fulfilling the following three premises: (1) their age-associated manifestation, (2) the acceleration of aging by experimentally accentuating them, and (3) the opportunity to decelerate, stop, or reverse aging by therapeutic interventions on them. We propose the following twelve hallmarks of aging: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, disabled macroautophagy, deregulated nutrient-sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, chronic inflammation, and dysbiosis. These hallmarks are interconnected among each other, as well as to the recently proposed hallmarks of health, which include organizational features of spatial compartmentalization, maintenance of homeostasis, and adequate responses to stress.

DOI: https://doi.org/10.1016/j.cell.2022.11.001
Elife. 2023 Jan 04. pii: e84295. [Epub ahead of print]12

Dynamic metabolome profiling uncovers potential TOR signaling genes.

Stella Reichling, Peter F Doubleday, Tomas Germade, Ariane Bergmann, Robbie Loewith, Uwe Sauer, Duncan Holbrook-Smith.

  Although the genetic code of the yeast Saccharomyces cerevisiae was sequenced 25 years ago, the characterization of the roles of genes within it is far from complete. The lack of a complete mapping of functions to genes hampers systematic understanding of the biology of the cell. The advent of high-throughput metabolomics offers a unique approach to uncovering gene function with an attractive combination of cost, robustness, and breadth of applicability. Here, we used flow-injection time-of-flight mass spectrometry to dynamically profile the metabolome of 164 loss-of-function mutants in TOR and receptor or receptor-like genes under a time course of rapamycin treatment, generating a dataset with >7000 metabolomics measurements. In order to provide a resource to the broader community, those data are made available for browsing through an interactive data visualization app hosted at https://rapamycin-yeast.ethz.ch. We demonstrate that dynamic metabolite responses to rapamycin are more informative than steady-state responses when recovering known regulators of TOR signaling, as well as identifying new ones. Deletion of a subset of the novel genes causes phenotypes and proteome responses to rapamycin that further implicate them in TOR signaling. We found that one of these genes, CFF1, was connected to the regulation of pyrimidine biosynthesis through URA10. These results demonstrate the efficacy of the approach for flagging novel potential TOR signaling-related genes and highlight the utility of dynamic perturbations when using functional metabolomics to deliver biological insight.

Keywords:  S. cerevisiae; TOR signaling; biochemistry; chemical biology; chemical genetics; metabolomics; systems biology

DOI:  https://doi.org/10.7554/eLife.84295