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Bousbaine D, Bauman KD, Chen YE, Yu VK, Lalgudi PV, Naziripour A, Veinbachs A, Phung JL, Nguyen TTD, Swenson JM, Lee YE, Dimas A, Jain S, Meng X, Pham TPT, Zhao A, Barkal L, Gribonika I, Van Rompay KKA, Belkaid Y, Barnes CO, Fischbach MA. Discovery and engineering of the antibody response against a prominent skin commensal. bioRxiv 2024:2024.01.23.576900. [PMID: 38328052 PMCID: PMC10849572 DOI: 10.1101/2024.01.23.576900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The ubiquitous skin colonist Staphylococcus epidermidis elicits a CD8 + T cell response pre-emptively, in the absence of an infection 1 . However, the scope and purpose of this anti-commensal immune program are not well defined, limiting our ability to harness it therapeutically. Here, we show that this colonist also induces a potent, durable, and specific antibody response that is conserved in humans and non-human primates. A series of S. epidermidis cell-wall mutants revealed that the cell surface protein Aap is a predominant target. By colonizing mice with a strain of S. epidermidis in which the parallel β-helix domain of Aap is replaced by tetanus toxin fragment C, we elicit a potent neutralizing antibody response that protects mice against a lethal challenge. A similar strain of S. epidermidis expressing an Aap-SpyCatcher chimera can be conjugated with recombinant immunogens; the resulting labeled commensal elicits high titers of antibody under conditions of physiologic colonization, including a robust IgA response in the nasal mucosa. Thus, immunity to a common skin colonist involves a coordinated T and B cell response, the latter of which can be redirected against pathogens as a novel form of topical vaccination.
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Gu X, Jouandin P, Lalgudi PV, Binari R, Valenstein ML, Reid MA, Allen AE, Kamitaki N, Locasale JW, Perrimon N, Sabatini DM. Author Correction: Sestrin mediates detection of and adaptation to low-leucine diets in Drosophila. Nature 2022; 609:E11. [PMID: 36100671 DOI: 10.1038/s41586-022-05286-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xin Gu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Patrick Jouandin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
| | - Pranav V Lalgudi
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rich Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Max L Valenstein
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael A Reid
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Annamarie E Allen
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Nolan Kamitaki
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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Gu X, Jouandin P, Lalgudi PV, Binari R, Valenstein ML, Reid MA, Allen AE, Kamitaki N, Locasale JW, Perrimon N, Sabatini DM. Sestrin mediates detection of and adaptation to low-leucine diets in Drosophila. Nature 2022; 608:209-216. [PMID: 35859173 PMCID: PMC10112710 DOI: 10.1038/s41586-022-04960-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/09/2022] [Indexed: 12/28/2022]
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) regulates cell growth and metabolism in response to multiple nutrients, including the essential amino acid leucine1. Recent work in cultured mammalian cells established the Sestrins as leucine-binding proteins that inhibit mTORC1 signalling during leucine deprivation2,3, but their role in the organismal response to dietary leucine remains elusive. Here we find that Sestrin-null flies (Sesn-/-) fail to inhibit mTORC1 or activate autophagy after acute leucine starvation and have impaired development and a shortened lifespan on a low-leucine diet. Knock-in flies expressing a leucine-binding-deficient Sestrin mutant (SesnL431E) have reduced, leucine-insensitive mTORC1 activity. Notably, we find that flies can discriminate between food with or without leucine, and preferentially feed and lay progeny on leucine-containing food. This preference depends on Sestrin and its capacity to bind leucine. Leucine regulates mTORC1 activity in glial cells, and knockdown of Sesn in these cells reduces the ability of flies to detect leucine-free food. Thus, nutrient sensing by mTORC1 is necessary for flies not only to adapt to, but also to detect, a diet deficient in an essential nutrient.
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Affiliation(s)
- Xin Gu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Patrick Jouandin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
| | - Pranav V Lalgudi
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rich Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Max L Valenstein
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael A Reid
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Annamarie E Allen
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Nolan Kamitaki
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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Valenstein ML, Rogala KB, Lalgudi PV, Brignole EJ, Gu X, Saxton RA, Chantranupong L, Kolibius J, Quast JP, Sabatini DM. Structure of the nutrient-sensing hub GATOR2. Nature 2022; 607:610-616. [PMID: 35831510 PMCID: PMC9464592 DOI: 10.1038/s41586-022-04939-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 06/07/2022] [Indexed: 02/04/2023]
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) controls growth by regulating anabolic and catabolic processes in response to environmental cues, including nutrients1,2. Amino acids signal to mTORC1 through the Rag GTPases, which are regulated by several protein complexes, including GATOR1 and GATOR2. GATOR2, which has five components (WDR24, MIOS, WDR59, SEH1L and SEC13), is required for amino acids to activate mTORC1 and interacts with the leucine and arginine sensors SESN2 and CASTOR1, respectively3-5. Despite this central role in nutrient sensing, GATOR2 remains mysterious as its subunit stoichiometry, biochemical function and structure are unknown. Here we used cryo-electron microscopy to determine the three-dimensional structure of the human GATOR2 complex. We found that GATOR2 adopts a large (1.1 MDa), two-fold symmetric, cage-like architecture, supported by an octagonal scaffold and decorated with eight pairs of WD40 β-propellers. The scaffold contains two WDR24, four MIOS and two WDR59 subunits circularized via two distinct types of junction involving non-catalytic RING domains and α-solenoids. Integration of SEH1L and SEC13 into the scaffold through β-propeller blade donation stabilizes the GATOR2 complex and reveals an evolutionary relationship to the nuclear pore and membrane-coating complexes6. The scaffold orients the WD40 β-propeller dimers, which mediate interactions with SESN2, CASTOR1 and GATOR1. Our work reveals the structure of an essential component of the nutrient-sensing machinery and provides a foundation for understanding the function of GATOR2 within the mTORC1 pathway.
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Affiliation(s)
- Max L Valenstein
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Kacper B Rogala
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Pranav V Lalgudi
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Edward J Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- MIT.nano, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xin Gu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert A Saxton
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lynne Chantranupong
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonas Kolibius
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
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Winters IP, Rogers ZN, McFarland CD, Lalgudi PV, Chiou SH, Kay MA, Petrov D, Winslow MM. Abstract IA03: Functional lung cancer genomics through in vivo genome editing. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-ia03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer genome sequencing has been instrumental in identifying the genomic alterations that occur in human tumors. However, the functional importance of the vast majority of these alterations, both alone and in combination, remains unknown. I will describe methods that integrate tumor barcoding with CRISPR/Cas9-mediated genome editing and ultradeep barcode sequencing to interrogate multiple tumor genotypes simultaneously in autochthonous mouse models of human cancer. We initially used this method to quantify the effects of eleven of the most frequently inactivated genes in human lung adenocarcinoma on tumor growth in vivo. We also investigated the in vivo fitness advantage conferred by inactivation of each of these eleven genes in combination with inactivation of p53 or Lkb1. This map of tumor-suppressive effects for >30 common lung adenocarcinoma genotypes revealed a complex landscape of context dependence and variability in effect strength. I will also describe a platform that integrates multiplexed Cas9-mediated homology-directed repair (HDR) with DNA barcoding and high-throughput sequencing to simultaneously investigate multiple oncogenic alterations in parallel. Using this approach, we introduced a library of nonsynonymous mutations into endogenous Kras in adult somatic cells to initiate tumors. High-throughput sequencing of barcoded Kras HDR alleles from bulk tumor-bearing lung uncovered surprising diversity in Kras variant oncogenicity. These in vivo approaches may redefine our ability to understand how diverse genomic alterations impact tumor initiation, growth, malignant transformation, and therapy responses.
Citation Format: Ian P. Winters, Zoë N. Rogers, Christopher D. McFarland, Pranav V. Lalgudi, Shin-Heng Chiou, Mark A. Kay, Dmitri Petrov, Monte M. Winslow. Functional lung cancer genomics through in vivo genome editing [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA03.
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Affiliation(s)
| | - Zoë N. Rogers
- Stanford University School of Medicine, Stanford, CA
| | | | | | | | - Mark A. Kay
- Stanford University School of Medicine, Stanford, CA
| | - Dmitri Petrov
- Stanford University School of Medicine, Stanford, CA
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Winters IP, Chiou SH, Paulk NK, McFarland CD, Lalgudi PV, Ma RK, Lisowski L, Connolly AJ, Petrov DA, Kay MA, Winslow MM. Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity. Nat Commun 2017; 8:2053. [PMID: 29233960 PMCID: PMC5727199 DOI: 10.1038/s41467-017-01519-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Large-scale genomic analyses of human cancers have cataloged somatic point mutations thought to initiate tumor development and sustain cancer growth. However, determining the functional significance of specific alterations remains a major bottleneck in our understanding of the genetic determinants of cancer. Here, we present a platform that integrates multiplexed AAV/Cas9-mediated homology-directed repair (HDR) with DNA barcoding and high-throughput sequencing to simultaneously investigate multiple genomic alterations in de novo cancers in mice. Using this approach, we introduce a barcoded library of non-synonymous mutations into hotspot codons 12 and 13 of Kras in adult somatic cells to initiate tumors in the lung, pancreas, and muscle. High-throughput sequencing of barcoded Kras HDR alleles from bulk lung and pancreas reveals surprising diversity in Kras variant oncogenicity. Rapid, cost-effective, and quantitative approaches to simultaneously investigate the function of precise genomic alterations in vivo will help uncover novel biological and clinically actionable insights into carcinogenesis.
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Affiliation(s)
- Ian P Winters
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shin-Heng Chiou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nicole K Paulk
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Pranav V Lalgudi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rosanna K Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Leszek Lisowski
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Translational Vectorology Group, Children's Medical Research Institute, Westmead, NSW, 2145, Australia
- Military Institute of Hygiene and Epidemiology, Puławy, 24-100, Poland
| | - Andrew J Connolly
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Mark A Kay
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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