1
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Köberlin MS, Fan Y, Liu C, Chung M, Pinto AFM, Jackson PK, Saghatelian A, Meyer T. A fast-acting lipid checkpoint in G1 prevents mitotic defects. Nat Commun 2024; 15:2441. [PMID: 38499565 PMCID: PMC10948896 DOI: 10.1038/s41467-024-46696-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Lipid synthesis increases during the cell cycle to ensure sufficient membrane mass, but how insufficient synthesis restricts cell-cycle entry is not understood. Here, we identify a lipid checkpoint in G1 phase of the mammalian cell cycle by using live single-cell imaging, lipidome, and transcriptome analysis of a non-transformed cell. We show that synthesis of fatty acids in G1 not only increases lipid mass but extensively shifts the lipid composition to unsaturated phospholipids and neutral lipids. Strikingly, acute lowering of lipid synthesis rapidly activates the PERK/ATF4 endoplasmic reticulum (ER) stress pathway that blocks cell-cycle entry by increasing p21 levels, decreasing Cyclin D levels, and suppressing Retinoblastoma protein phosphorylation. Together, our study identifies a rapid anticipatory ER lipid checkpoint in G1 that prevents cells from starting the cell cycle as long as lipid synthesis is low, thereby preventing mitotic defects, which are triggered by low lipid synthesis much later in mitosis.
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Affiliation(s)
- Marielle S Köberlin
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Chad Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94111, USA
| | - Mingyu Chung
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
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2
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Boegholm N, Petriman NA, Loureiro‐López M, Wang J, Vela MIS, Liu B, Kanie T, Ng R, Jackson PK, Andersen JS, Lorentzen E. The IFT81-IFT74 complex acts as an unconventional RabL2 GTPase-activating protein during intraflagellar transport. EMBO J 2023; 42:e111807. [PMID: 37606072 PMCID: PMC10505919 DOI: 10.15252/embj.2022111807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/24/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Cilia are important cellular organelles for signaling and motility and are constructed via intraflagellar transport (IFT). RabL2 is a small GTPase that localizes to the basal body of cilia via an interaction with the centriolar protein CEP19 before downstream association with the IFT machinery, which is followed by initiation of IFT. We reconstituted and purified RabL2 with CEP19 or IFT proteins to show that a reconstituted pentameric IFT complex containing IFT81/74 enhances the GTP hydrolysis rate of RabL2. The binding site on IFT81/74 that promotes GTP hydrolysis in RabL2 was mapped to a 70-amino-acid-long coiled-coil region of IFT81/74. We present structural models for RabL2-containing IFT complexes that we validate in vitro and in cellulo and demonstrate that Chlamydomonas IFT81/74 enhances GTP hydrolysis of human RabL2, suggesting an ancient evolutionarily conserved activity. Our results provide an architectural understanding of how RabL2 is incorporated into the IFT complex and a molecular rationale for why RabL2 dissociates from anterograde IFT trains soon after departure from the ciliary base.
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Affiliation(s)
- Niels Boegholm
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | - Narcis A Petriman
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | - Marta Loureiro‐López
- Department for Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Jiaolong Wang
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
| | | | - Beibei Liu
- Department of Cell BiologyUniversity of Oklahoma Health Science CenterOklahomaOKUSA
| | - Tomoharu Kanie
- Department of Cell BiologyUniversity of Oklahoma Health Science CenterOklahomaOKUSA
- Baxter Laboratory, Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
| | - Roy Ng
- Baxter Laboratory, Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Jens S Andersen
- Department for Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Esben Lorentzen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhus CDenmark
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3
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Kostyrko K, Román M, Lee AG, Simpson DR, Dinh PT, Leung SG, Marini KD, Kelly MR, Broyde J, Califano A, Jackson PK, Sweet-Cordero EA. UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma. Nat Commun 2023; 14:3966. [PMID: 37407562 PMCID: PMC10322837 DOI: 10.1038/s41467-023-39591-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
KRAS is a frequent driver in lung cancer. To identify KRAS-specific vulnerabilities in lung cancer, we performed RNAi screens in primary spheroids derived from a Kras mutant mouse lung cancer model and discovered an epigenetic regulator Ubiquitin-like containing PHD and RING finger domains 1 (UHRF1). In human lung cancer models UHRF1 knock-out selectively impaired growth and induced apoptosis only in KRAS mutant cells. Genome-wide methylation and gene expression analysis of UHRF1-depleted KRAS mutant cells revealed global DNA hypomethylation leading to upregulation of tumor suppressor genes (TSGs). A focused CRISPR/Cas9 screen validated several of these TSGs as mediators of UHRF1-driven tumorigenesis. In vivo, UHRF1 knock-out inhibited tumor growth of KRAS-driven mouse lung cancer models. Finally, in lung cancer patients high UHRF1 expression is anti-correlated with TSG expression and predicts worse outcomes for patients with KRAS mutant tumors. These results nominate UHRF1 as a KRAS-specific vulnerability and potential target for therapeutic intervention.
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Affiliation(s)
- Kaja Kostyrko
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
| | - Marta Román
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Alex G Lee
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - David R Simpson
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Phuong T Dinh
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Stanley G Leung
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Kieren D Marini
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Marcus R Kelly
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joshua Broyde
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - E Alejandro Sweet-Cordero
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
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4
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Weiss LE, Love JF, Yoon J, Comerci CJ, Milenkovic L, Kanie T, Jackson PK, Stearns T, Gustavsson AK. Single-molecule imaging in the primary cilium. Methods Cell Biol 2023; 176:59-83. [PMID: 37164543 PMCID: PMC10509820 DOI: 10.1016/bs.mcb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The primary cilium is an important signaling organelle critical for normal development and tissue homeostasis. Its small dimensions and complexity necessitate advanced imaging approaches to uncover the molecular mechanisms behind its function. Here, we outline how single-molecule fluorescence microscopy can be used for tracking molecular dynamics and interactions and for super-resolution imaging of nanoscale structures in the primary cilium. Specifically, we describe in detail how to capture and quantify the 2D dynamics of individual transmembrane proteins PTCH1 and SMO and how to map the 3D nanoscale distributions of the inversin compartment proteins INVS, ANKS6, and NPHP3. This protocol can, with minor modifications, be adapted for studies of other proteins and cell lines to further elucidate the structure and function of the primary cilium at the molecular level.
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Affiliation(s)
- Lucien E Weiss
- Department of Engineering Physics, Polytechnique Montréal, Montreal, QC, Canada.
| | - Julia F Love
- Department of Chemistry, Rice University, Houston, TX, United States
| | | | - Colin J Comerci
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
| | | | - Tomoharu Kanie
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States; Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA, United States; Rockefeller University, New York City, NY, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States; Department of BioSciences, Rice University, Houston, TX, United States; Institute of Biosciences and Bioengineering, Rice University, Houston, TX, United States; Smalley-Curl Institute, Rice University, Houston, TX, United States.
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5
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Kanie T, Ng R, Abbott KL, Pongs O, Jackson PK. Myristoylated Neuronal Calcium Sensor-1 captures the ciliary vesicle at distal appendages. bioRxiv 2023:2023.01.06.523037. [PMID: 36712037 PMCID: PMC9881967 DOI: 10.1101/2023.01.06.523037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The primary cilium is a microtubule-based organelle that cycles through assembly and disassembly. In many cell types, formation of the cilium is initiated by recruitment of ciliary vesicles to the distal appendage of the mother centriole. However, the distal appendage mechanism that directly captures ciliary vesicles is yet to be identified. In an accompanying paper, we show that the distal appendage protein, CEP89, is important for thef ciliary vesicle recruitment, but not for other steps of cilium formation (Tomoharu Kanie, Love, Fisher, Gustavsson, & Jackson, 2023). The lack of a membrane binding motif in CEP89 suggests that it may indirectly recruit ciliary vesicles via another binding partner. Here, we identify Neuronal Calcium Sensor-1 (NCS1) as a stoichiometric interactor of CEP89. NCS1 localizes to the position between CEP89 and a ciliary vesicle marker, RAB34, at the distal appendage. This localization was completely abolished in CEP89 knockouts, suggesting that CEP89 recruits NCS1 to the distal appendage. Similarly to CEP89 knockouts, ciliary vesicle recruitment as well as subsequent cilium formation was perturbed in NCS1 knockout cells. The ability of NCS1 to recruit the ciliary vesicle is dependent on its myristoylation motif and NCS1 knockout cells expressing myristoylation defective mutant failed to rescue the vesicle recruitment defect despite localizing proper localization to the centriole. In sum, our analysis reveals the first known mechanism for how the distal appendage recruits the ciliary vesicles.
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Affiliation(s)
- Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK, 73112
| | - Roy Ng
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
| | - Keene L. Abbott
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
| | - Olaf Pongs
- Institute for Physiology, Center for Integrative Physiology and Molecular Medicine (CIPPM), Saarland University, Homburg, Germany
| | - Peter K. Jackson
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
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6
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Kanie T, Love JF, Fisher SD, Gustavsson AK, Jackson PK. A hierarchical pathway for assembly of the distal appendages that organize primary cilia. bioRxiv 2023:2023.01.06.522944. [PMID: 36711481 PMCID: PMC9881904 DOI: 10.1101/2023.01.06.522944] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Distal appendages are nine-fold symmetric blade-like structures attached to the distal end of the mother centriole. These structures are critical for formation of the primary cilium, by regulating at least four critical steps: ciliary vesicle recruitment, recruitment and initiation of intraflagellar transport (IFT), and removal of CP110. While specific proteins that localize to the distal appendages have been identified, how exactly each protein functions to achieve the multiple roles of the distal appendages is poorly understood. Here we comprehensively analyze known and newly discovered distal appendage proteins (CEP83, SCLT1, CEP164, TTBK2, FBF1, CEP89, KIZ, ANKRD26, PIDD1, LRRC45, NCS1, C3ORF14) for their precise localization, order of recruitment, and their roles in each step of cilia formation. Using CRISPR-Cas9 knockouts, we show that the order of the recruitment of the distal appendage proteins is highly interconnected and a more complex hierarchy. Our analysis highlights two protein modules, CEP83-SCLT1 and CEP164-TTBK2, as critical for structural assembly of distal appendages. Functional assay revealed that CEP89 selectively functions in RAB34+ ciliary vesicle recruitment, while deletion of the integral components, CEP83-SCLT1-CEP164-TTBK2, severely compromised all four steps of cilium formation. Collectively, our analyses provide a more comprehensive view of the organization and the function of the distal appendage, paving the way for molecular understanding of ciliary assembly.
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Affiliation(s)
- Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK, 73112
| | - Julia F. Love
- Department of Chemistry, Rice University, Houston, TX, 77005
| | | | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, 77005
- Department of BioSciences, Rice University, Houston, TX, 77005
- Smalley-Curl Institute, Rice University, Houston, TX, 77005
- Institute of Biosciences and Bioengineering, Rice University, Houston, TX, 77005
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Peter K. Jackson
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
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7
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Wu CT, Lidsky PV, Xiao Y, Cheng R, Lee IT, Nakayama T, Jiang S, He W, Demeter J, Knight MG, Turn RE, Rojas-Hernandez LS, Ye C, Chiem K, Shon J, Martinez-Sobrido L, Bertozzi CR, Nolan GP, Nayak JV, Milla C, Andino R, Jackson PK. SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. Cell 2023; 186:112-130.e20. [PMID: 36580912 PMCID: PMC9715480 DOI: 10.1016/j.cell.2022.11.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 09/15/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
Abstract
How SARS-CoV-2 penetrates the airway barrier of mucus and periciliary mucins to infect nasal epithelium remains unclear. Using primary nasal epithelial organoid cultures, we found that the virus attaches to motile cilia via the ACE2 receptor. SARS-CoV-2 traverses the mucus layer, using motile cilia as tracks to access the cell body. Depleting cilia blocks infection for SARS-CoV-2 and other respiratory viruses. SARS-CoV-2 progeny attach to airway microvilli 24 h post-infection and trigger formation of apically extended and highly branched microvilli that organize viral egress from the microvilli back into the mucus layer, supporting a model of virus dispersion throughout airway tissue via mucociliary transport. Phosphoproteomics and kinase inhibition reveal that microvillar remodeling is regulated by p21-activated kinases (PAK). Importantly, Omicron variants bind with higher affinity to motile cilia and show accelerated viral entry. Our work suggests that motile cilia, microvilli, and mucociliary-dependent mucus flow are critical for efficient virus replication in nasal epithelia.
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Affiliation(s)
- Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, Room S572E, Box 2280, San Francisco, CA, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, Room S572E, Box 2280, San Francisco, CA, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA; Department of Biology, Stanford University, Stanford, CA, USA
| | - Ivan T Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Tsuguhisa Nakayama
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wei He
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA
| | - Miguel G Knight
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, Room S572E, Box 2280, San Francisco, CA, USA
| | - Rachel E Turn
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA
| | - Laura S Rojas-Hernandez
- Department of Pediatric Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Chengjin Ye
- Disease Intervention and Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Kevin Chiem
- Disease Intervention and Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Judy Shon
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Luis Martinez-Sobrido
- Disease Intervention and Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Otolaryngology, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Carlos Milla
- Department of Pediatric Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, Room S572E, Box 2280, San Francisco, CA, USA.
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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8
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Tang R, Shuldiner EG, Kelly M, Murray CW, Hebert JD, Andrejka L, Tsai MK, Hughes NW, Parker MI, Cai H, Li YC, Wahl GM, Dunbrack RL, Jackson PK, Petrov DA, Winslow MM. Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth. Nat Cell Biol 2023; 25:159-169. [PMID: 36635501 PMCID: PMC10521195 DOI: 10.1038/s41556-022-01049-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 09/13/2021] [Accepted: 11/09/2022] [Indexed: 01/13/2023]
Abstract
Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the regulators of RAS signalling is incomplete. Here to uncover the impact of diverse KRAS-interacting proteins on lung cancer growth, we combined multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumour barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung cancer models, we show that HRAS and NRAS are suppressors of KRASG12D-driven tumour growth in vivo and confirm these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogues interact with oncogenic KRAS, suppress KRAS-KRAS interactions, and reduce downstream ERK signalling. Furthermore, HRAS and NRAS mutations identified in oncogenic KRAS-driven human tumours partially abolished this effect. By comparing the tumour-suppressive effects of HRAS and NRAS in oncogenic KRAS- and oncogenic BRAF-driven lung cancer models, we confirm that RAS paralogues are specific suppressors of KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role RAS paralogue imbalance in oncogenic KRAS-driven lung cancer.
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Affiliation(s)
- Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Marcus Kelly
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Baxter Laboratories, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher W Murray
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Jess D Hebert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas W Hughes
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mitchell I Parker
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
- Molecular and Cell Biology and Genetics Program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yao-Cheng Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roland L Dunbrack
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peter K Jackson
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Baxter Laboratories, Stanford University School of Medicine, Stanford, CA, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- The Chan Zuckerberg BioHub, San Francisco, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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9
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Janas JA, Zhang L, Luu JH, Demeter J, Meng L, Marro SG, Mall M, Mooney NA, Schaukowitch K, Ng YH, Yang N, Huang Y, Neumayer G, Gozani O, Elias JE, Jackson PK, Wernig M. Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation. Mol Cell 2022; 82:4627-4646.e14. [PMID: 36417913 PMCID: PMC9779922 DOI: 10.1016/j.molcel.2022.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
Cell lineage specification is accomplished by a concerted action of chromatin remodeling and tissue-specific transcription factors. However, the mechanisms that induce and maintain appropriate lineage-specific gene expression remain elusive. Here, we used an unbiased proteomics approach to characterize chromatin regulators that mediate the induction of neuronal cell fate. We found that Tip60 acetyltransferase is essential to establish neuronal cell identity partly via acetylation of the histone variant H2A.Z. Despite its tight correlation with gene expression and active chromatin, loss of H2A.Z acetylation had little effect on chromatin accessibility or transcription. Instead, loss of Tip60 and acetyl-H2A.Z interfered with H3K4me3 deposition and activation of a unique subset of silent, lineage-restricted genes characterized by a bivalent chromatin configuration at their promoters. Altogether, our results illuminate the mechanisms underlying bivalent chromatin activation and reveal that H2A.Z acetylation regulates neuronal fate specification by establishing epigenetic competence for bivalent gene activation and cell lineage transition.
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Affiliation(s)
- Justyna A Janas
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lichao Zhang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacklyn H Luu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lingjun Meng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samuele G Marro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Moritz Mall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katie Schaukowitch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yi Han Ng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nan Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuhao Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gernot Neumayer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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10
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Porpiglia E, Mai T, Kraft P, Holbrook CA, de Morree A, Gonzalez VD, Hilgendorf KI, Frésard L, Trejo A, Bhimaraju S, Jackson PK, Fantl WJ, Blau HM. Elevated CD47 is a hallmark of dysfunctional aged muscle stem cells that can be targeted to augment regeneration. Cell Stem Cell 2022; 29:1653-1668.e8. [PMID: 36384141 PMCID: PMC9746883 DOI: 10.1016/j.stem.2022.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/04/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022]
Abstract
In aging, skeletal muscle strength and regenerative capacity decline, due in part to functional impairment of muscle stem cells (MuSCs), yet the underlying mechanisms remain elusive. Here, we capitalize on mass cytometry to identify high CD47 expression as a hallmark of dysfunctional MuSCs (CD47hi) with impaired regenerative capacity that predominate with aging. The prevalent CD47hi MuSC subset suppresses the residual functional CD47lo MuSC subset through a paracrine signaling loop, leading to impaired proliferation. We uncover that elevated CD47 levels on aged MuSCs result from increased U1 snRNA expression, which disrupts alternative polyadenylation. The deficit in aged MuSC function in regeneration can be overcome either by morpholino-mediated blockade of CD47 alternative polyadenylation or antibody blockade of thrombospondin-1/CD47 signaling, leading to improved regeneration in aged mice, with therapeutic implications. Our findings highlight a previously unrecognized age-dependent alteration in CD47 levels and function in MuSCs, which underlies reduced muscle repair in aging.
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Affiliation(s)
- Ermelinda Porpiglia
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark.
| | - Thach Mai
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peggy Kraft
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Colin A Holbrook
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine de Morree
- Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Veronica D Gonzalez
- Nolan Laboratory, Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keren I Hilgendorf
- Jackson Laboratory, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laure Frésard
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Angelica Trejo
- Nolan Laboratory, Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Sriram Bhimaraju
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Jackson Laboratory, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wendy J Fantl
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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11
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Schmidt HB, Jaafar ZA, Wulff BE, Rodencal JJ, Hong K, Aziz-Zanjani MO, Jackson PK, Leonetti MD, Dixon SJ, Rohatgi R, Brandman O. Oxaliplatin disrupts nucleolar function through biophysical disintegration. Cell Rep 2022; 41:111629. [DOI: 10.1016/j.celrep.2022.111629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 08/28/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
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12
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Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. J Exp Med 2022; 219:213217. [PMID: 35551368 PMCID: PMC9111091 DOI: 10.1084/jem.20201405] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Inborn errors of immunity (IEIs) unveil regulatory pathways of human immunity. We describe a new IEI caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene in patients with infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis. Patients and Gimap6−/− mice show defects in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)–containing lipids. We find that GIMAP6 complexes with GABARAPL2 and GIMAP7 to regulate GTPase activity. Also, GIMAP6 is induced by IFN-γ and plays a critical role in antibacterial immunity. Finally, we observed that Gimap6−/− mice died prematurely from microangiopathic glomerulosclerosis most likely due to GIMAP6 deficiency in kidney endothelial cells.
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Affiliation(s)
- Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ping Du Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Brittany N Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Deniz Cagdas
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Arasu Balasubramaniyam
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Bella Shadur
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel.,The Garvan Institute of Medical Research, Immunology Division, Darlinghurst, Sydney, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, Australia
| | - Adeeb NaserEddin
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Les R Folio
- Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Simone Gottlieb
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Michael A Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ilhan Tezcan
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Akdogan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Sevgen Onder
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Avi Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Errin Johnson
- The Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Peter K Jackson
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Janos Demeter
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Florian Paul
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias Selbach
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Haydar Bulut
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Catharine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Polina Stepensky
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - John C Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
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13
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Mascharak S, Talbott HE, Januszyk M, Griffin M, Chen K, Davitt MF, Demeter J, Henn D, Bonham CA, Foster DS, Mooney N, Cheng R, Jackson PK, Wan DC, Gurtner GC, Longaker MT. Multi-omic analysis reveals divergent molecular events in scarring and regenerative wound healing. Cell Stem Cell 2022; 29:315-327.e6. [DOI: 10.1016/j.stem.2021.12.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 07/01/2021] [Accepted: 12/22/2021] [Indexed: 02/01/2023]
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14
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Xiao Y, Lidsky PV, Shirogane Y, Aviner R, Wu CT, Li W, Zheng W, Talbot D, Catching A, Doitsh G, Su W, Gekko CE, Nayak A, Ernst JD, Brodsky L, Brodsky E, Rousseau E, Capponi S, Bianco S, Nakamura R, Jackson PK, Frydman J, Andino R. A defective viral genome strategy elicits broad protective immunity against respiratory viruses. Cell 2021; 184:6037-6051.e14. [PMID: 34852237 PMCID: PMC8598942 DOI: 10.1016/j.cell.2021.11.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022]
Abstract
RNA viruses generate defective viral genomes (DVGs) that can interfere with replication of the parental wild-type virus. To examine their therapeutic potential, we created a DVG by deleting the capsid-coding region of poliovirus. Strikingly, intraperitoneal or intranasal administration of this genome, which we termed eTIP1, elicits an antiviral response, inhibits replication, and protects mice from several RNA viruses, including enteroviruses, influenza, and SARS-CoV-2. While eTIP1 replication following intranasal administration is limited to the nasal cavity, its antiviral action extends non-cell-autonomously to the lungs. eTIP1 broad-spectrum antiviral effects are mediated by both local and distal type I interferon responses. Importantly, while a single eTIP1 dose protects animals from SARS-CoV-2 infection, it also stimulates production of SARS-CoV-2 neutralizing antibodies that afford long-lasting protection from SARS-CoV-2 reinfection. Thus, eTIP1 is a safe and effective broad-spectrum antiviral generating short- and long-term protection against SARS-CoV-2 and other respiratory infections in animal models.
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Affiliation(s)
- Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuta Shirogane
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Ranen Aviner
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Chien-Ting Wu
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Weiyi Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Weihao Zheng
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Dale Talbot
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Aleph Therapeutics, Inc., Stanford, CA 94305, USA
| | - Adam Catching
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gilad Doitsh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Weiheng Su
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; School of Life Sciences, Jilin University, Changchun, China
| | - Colby E Gekko
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Arabinda Nayak
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joel D Ernst
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center and Department of Evolutionary & Environmental Biology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | | | - Elsa Rousseau
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Sara Capponi
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Simone Bianco
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | | | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
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15
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Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. Structured elements drive extensive circular RNA translation. Mol Cell 2021; 81:4300-4318.e13. [PMID: 34437836 PMCID: PMC8567535 DOI: 10.1016/j.molcel.2021.07.042] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022]
Abstract
The human genome encodes tens of thousands circular RNAs (circRNAs) with mostly unknown functions. Circular RNAs require internal ribosome entry sites (IRES) if they are to undergo translation without a 5' cap. Here, we develop a high-throughput screen to systematically discover RNA sequences that can direct circRNA translation in human cells. We identify more than 17,000 endogenous and synthetic sequences as candidate circRNA IRES. 18S rRNA complementarity and a structured RNA element positioned on the IRES are important for driving circRNA translation. Ribosome profiling and peptidomic analyses show extensive IRES-ribosome association, hundreds of circRNA-encoded proteins with tissue-specific distribution, and antigen presentation. We find that circFGFR1p, a protein encoded by circFGFR1 that is downregulated in cancer, functions as a negative regulator of FGFR1 oncoprotein to suppress cell growth during stress. Systematic identification of circRNA IRES elements may provide important links among circRNA regulation, biological function, and disease.
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Affiliation(s)
- Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shira Weingarten-Gabbay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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16
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Nakayama T, Lee IT, Jiang S, Matter MS, Yan CH, Overdevest JB, Wu CT, Goltsev Y, Shih LC, Liao CK, Zhu B, Bai Y, Lidsky P, Xiao Y, Zarabanda D, Yang A, Easwaran M, Schürch CM, Chu P, Chen H, Stalder AK, McIlwain DR, Borchard NA, Gall PA, Dholakia SS, Le W, Xu L, Tai CJ, Yeh TH, Erickson-Direnzo E, Duran JM, Mertz KD, Hwang PH, Haslbauer JD, Jackson PK, Menter T, Andino R, Canoll PD, DeConde AS, Patel ZM, Tzankov A, Nolan GP, Nayak JV. Determinants of SARS-CoV-2 entry and replication in airway mucosal tissue and susceptibility in smokers. Cell Rep Med 2021; 2:100421. [PMID: 34604819 PMCID: PMC8479532 DOI: 10.1016/j.xcrm.2021.100421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/21/2021] [Accepted: 09/22/2021] [Indexed: 02/07/2023]
Abstract
Understanding viral tropism is an essential step toward reducing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, decreasing mortality from coronavirus disease 2019 (COVID-19) and limiting opportunities for mutant strains to arise. Currently, little is known about the extent to which distinct tissue sites in the human head and neck region and proximal respiratory tract selectively permit SARS-CoV-2 infection and replication. In this translational study, we discover key variabilities in expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2), essential SARS-CoV-2 entry factors, among the mucosal tissues of the human proximal airways. We show that SARS-CoV-2 infection is present in all examined head and neck tissues, with a notable tropism for the nasal cavity and tracheal mucosa. Finally, we uncover an association between smoking and higher SARS-CoV-2 viral infection in the human proximal airway, which may explain the increased susceptibility of smokers to developing severe COVID-19. This is at least partially explained by differences in interferon (IFN)-β1 levels between smokers and non-smokers.
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Affiliation(s)
- Tsuguhisa Nakayama
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Ivan T. Lee
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Matthias S. Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Carol H. Yan
- Division of Otolaryngology – Head and Neck Surgery, Department of Surgery, University of California San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan B. Overdevest
- Department of Otolaryngology–Head and Neck Surgery, Columbia University School of Medicine, New York, NY, USA
| | - Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang-Chun Shih
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Chun-Kang Liao
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Bokai Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - David Zarabanda
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Angela Yang
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Meena Easwaran
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Christian M. Schürch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna K. Stalder
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - David R. McIlwain
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole A. Borchard
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Phillip A. Gall
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Sachi S. Dholakia
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Wei Le
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Le Xu
- Department of Pediatrics, University of California San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chih-Jaan Tai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Te-Huei Yeh
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Elizabeth Erickson-Direnzo
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Jason M. Duran
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kirsten D. Mertz
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Peter H. Hwang
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Jasmin D. Haslbauer
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Peter K. Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas Menter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Peter D. Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, Irving Cancer Research Center, New York, NY, USA
| | - Adam S. DeConde
- Division of Otolaryngology – Head and Neck Surgery, Department of Surgery, University of California San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zara M. Patel
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Garry P. Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jayakar V. Nayak
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otolaryngology – Head and Neck Surgery, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
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17
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Abstract
[Figure: see text].
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Affiliation(s)
- Ran Cheng
- Department of Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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18
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Li X, Lidsky PV, Xiao Y, Wu CT, Garcia-Knight M, Yang J, Nakayama T, Nayak JV, Jackson PK, Andino R, Shu X. Ethacridine inhibits SARS-CoV-2 by inactivating viral particles. PLoS Pathog 2021; 17:e1009898. [PMID: 34478458 PMCID: PMC8445489 DOI: 10.1371/journal.ppat.1009898] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 03/08/2021] [Revised: 09/16/2021] [Accepted: 08/16/2021] [Indexed: 01/29/2023] Open
Abstract
The respiratory disease COVID-19 is caused by the coronavirus SARS-CoV-2. Here we report the discovery of ethacridine as a potent drug against SARS-CoV-2 (EC50 ~ 0.08 μM). Ethacridine was identified via high-throughput screening of an FDA-approved drug library in living cells using a fluorescence assay. Plaque assays, RT-PCR and immunofluorescence imaging at various stages of viral infection demonstrate that the main mode of action of ethacridine is through inactivation of viral particles, preventing their binding to the host cells. Consistently, ethacridine is effective in various cell types, including primary human nasal epithelial cells that are cultured in an air-liquid interface. Taken together, our work identifies a promising, potent, and new use of the old drug via a distinct mode of action for inhibiting SARS-CoV-2.
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Affiliation(s)
- Xiaoquan Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Peter V. Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Chien-Ting Wu
- Department of Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, California, United States of America
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Tsuguhisa Nakayama
- Department of Otolaryngology–Head and Neck Surgery, Stanford University, Stanford, California, United States of America
| | - Jayakar V. Nayak
- Department of Otolaryngology–Head and Neck Surgery, Stanford University, Stanford, California, United States of America
| | - Peter K. Jackson
- Department of Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, California, United States of America
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
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19
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Wu CT, Hilgendorf KI, Bevacqua RJ, Hang Y, Demeter J, Kim SK, Jackson PK. Discovery of ciliary G protein-coupled receptors regulating pancreatic islet insulin and glucagon secretion. Genes Dev 2021; 35:1243-1255. [PMID: 34385262 PMCID: PMC8415323 DOI: 10.1101/gad.348261.121] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 07/02/2021] [Indexed: 01/17/2023]
Abstract
Multiple G protein-coupled receptors (GPCRs) are expressed in pancreatic islet cells, but the majority have unknown functions. We observed specific GPCRs localized to primary cilia, a prominent signaling organelle, in pancreatic α and β cells. Loss of cilia disrupts β-cell endocrine function, but the molecular drivers are unknown. Using functional expression, we identified multiple GPCRs localized to cilia in mouse and human islet α and β cells, including FFAR4, PTGER4, ADRB2, KISS1R, and P2RY14. Free fatty acid receptor 4 (FFAR4) and prostaglandin E receptor 4 (PTGER4) agonists stimulate ciliary cAMP signaling and promote glucagon and insulin secretion by α- and β-cell lines and by mouse and human islets. Transport of GPCRs to primary cilia requires TULP3, whose knockdown in primary human and mouse islets relocalized ciliary FFAR4 and PTGER4 and impaired regulated glucagon or insulin secretion, without affecting ciliary structure. Our findings provide index evidence that regulated hormone secretion by islet α and β cells is controlled by ciliary GPCRs providing new targets for diabetes.
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Affiliation(s)
- Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Keren I Hilgendorf
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Medicine, Stanford University, Stanford, California 94305, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Medicine, Stanford University, Stanford, California 94305, USA
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20
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Wu CT, Lidsky PV, Xiao Y, Lee IT, Cheng R, Nakayama T, Jiang S, Demeter J, Bevacqua RJ, Chang CA, Whitener RL, Stalder AK, Zhu B, Chen H, Goltsev Y, Tzankov A, Nayak JV, Nolan GP, Matter MS, Andino R, Jackson PK. SARS-CoV-2 infects human pancreatic β cells and elicits β cell impairment. Cell Metab 2021; 33:1565-1576.e5. [PMID: 34081912 PMCID: PMC8130512 DOI: 10.1016/j.cmet.2021.05.013] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/01/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023]
Abstract
Emerging evidence points toward an intricate relationship between the pandemic of coronavirus disease 2019 (COVID-19) and diabetes. While preexisting diabetes is associated with severe COVID-19, it is unclear whether COVID-19 severity is a cause or consequence of diabetes. To mechanistically link COVID-19 to diabetes, we tested whether insulin-producing pancreatic β cells can be infected by SARS-CoV-2 and cause β cell depletion. We found that the SARS-CoV-2 receptor, ACE2, and related entry factors (TMPRSS2, NRP1, and TRFC) are expressed in β cells, with selectively high expression of NRP1. We discovered that SARS-CoV-2 infects human pancreatic β cells in patients who succumbed to COVID-19 and selectively infects human islet β cells in vitro. We demonstrated that SARS-CoV-2 infection attenuates pancreatic insulin levels and secretion and induces β cell apoptosis, each rescued by NRP1 inhibition. Phosphoproteomic pathway analysis of infected islets indicates apoptotic β cell signaling, similar to that observed in type 1 diabetes (T1D). In summary, our study shows SARS-CoV-2 can directly induce β cell killing.
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Affiliation(s)
- Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ivan T Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA, USA
| | - Tsuguhisa Nakayama
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles A Chang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Robert L Whitener
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna K Stalder
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland
| | - Bokai Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandar Tzankov
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthias S Matter
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
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21
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Nano PR, Johnson TK, Kudo T, Mooney NA, Ni J, Demeter J, Jackson PK, Chen JK. Structure-activity mapping of ARHGAP36 reveals regulatory roles for its GAP homology and C-terminal domains. PLoS One 2021; 16:e0251684. [PMID: 33999959 PMCID: PMC8128262 DOI: 10.1371/journal.pone.0251684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/11/2021] [Accepted: 05/01/2021] [Indexed: 11/24/2022] Open
Abstract
ARHGAP36 is an atypical Rho GTPase-activating protein (GAP) family member that drives both spinal cord development and tumorigenesis, acting in part through an N-terminal motif that suppresses protein kinase A and activates Gli transcription factors. ARHGAP36 also contains isoform-specific N-terminal sequences, a central GAP-like module, and a unique C-terminal domain, and the functions of these regions remain unknown. Here we have mapped the ARHGAP36 structure-activity landscape using a deep sequencing-based mutagenesis screen and truncation mutant analyses. Using this approach, we have discovered several residues in the GAP homology domain that are essential for Gli activation and a role for the C-terminal domain in counteracting an N-terminal autoinhibitory motif that is present in certain ARHGAP36 isoforms. In addition, each of these sites modulates ARHGAP36 recruitment to the plasma membrane or primary cilium. Through comparative proteomics, we also have identified proteins that preferentially interact with active ARHGAP36, and we demonstrate that one binding partner, prolyl oligopeptidase-like protein, is a novel ARHGAP36 antagonist. Our work reveals multiple modes of ARHGAP36 regulation and establishes an experimental framework that can be applied towards other signaling proteins.
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Affiliation(s)
- Patricia R. Nano
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Taylor K. Johnson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nancie A. Mooney
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jun Ni
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Janos Demeter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter K. Jackson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - James K. Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- * E-mail:
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22
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Abstract
Cyclic-3',5'-adenosine monophosphate (cAMP) is an ancient second messenger but organizing signaling selectivity on the nanoscale is poorly understood. Examining transport of a new fluorescent cAMP probe, Bock and coworkers observe "buffered diffusion" and establish phosphodiesterase activity can organize cAMP nanodomains, while Zhao and coworkers find that protein kinase A regulatory subunits assemble liquid droplets to further localize cAMP signaling.
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Affiliation(s)
- Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA.
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23
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Kanie T, Jackson PK. Connecting autoimmune disease to Bardet-Biedl syndrome and primary cilia. EMBO Rep 2021; 22:e52180. [PMID: 33511755 DOI: 10.15252/embr.202052180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/16/2020] [Indexed: 12/26/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a genetic disorder caused by the dysfunction of the primary cilium. To date, immunological defects in the disease have not been systematically assessed. In this issue, Tsyklauri and colleagues find, through detailed analysis of BBS mutant animals, that B-cell development is altered in mutant mice (Tsyklauri et al, 2021). The authors further report that BBS patients are more susceptible to autoimmune disorders. This study sheds new light on the potential role of primary cilia in controlling immune function in disease.
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Affiliation(s)
- Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
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24
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Li X, Lidsky P, Xiao Y, Wu CT, GarciaKnight M, Yang J, Nakayama T, Nayak JV, Jackson PK, Andino R, Shu X. Ethacridine inhibits SARS-CoV-2 by inactivating viral particles in cellular models. bioRxiv 2020:2020.10.28.359042. [PMID: 33140048 PMCID: PMC7605555 DOI: 10.1101/2020.10.28.359042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 is the coronavirus that causes the respiratory disease COVID-19, which is now the third-leading cause of death in the United States. The FDA has recently approved remdesivir, an inhibitor of SARS-CoV-2 replication, to treat COVID-19, though recent data from the WHO shows little to no benefit with use of this anti-viral agent. Here we report the discovery of ethacridine, a safe antiseptic use in humans, as a potent drug for use against SARS-CoV-2 (EC50 ~ 0.08 μM). Ethacridine was identified via high-throughput screening of an FDA-approved drug library in living cells using a fluorescent assay. Interestingly, the main mode of action of ethacridine is through inactivation of viral particles, preventing their binding to the host cells. Indeed, ethacridine is effective in various cell types, including primary human nasal epithelial cells. Taken together, these data identify a promising, potent, and new use of the old drug possessing a distinct mode of action for inhibiting SARS-CoV-2.
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Affiliation(s)
- Xiaoquan Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Peter Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Chien-Ting Wu
- Department of Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, California, USA
| | - Miguel GarciaKnight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
| | - Tsuguhisa Nakayama
- Department of Otolaryngology-Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Jayakar V. Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford University, Stanford, California, USA
| | - Peter K. Jackson
- Department of Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, California, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
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25
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Lee IT, Nakayama T, Wu CT, Goltsev Y, Jiang S, Gall PA, Liao CK, Shih LC, Schürch CM, McIlwain DR, Chu P, Borchard NA, Zarabanda D, Dholakia SS, Yang A, Kim D, Chen H, Kanie T, Lin CD, Tsai MH, Phillips KM, Kim R, Overdevest JB, Tyler MA, Yan CH, Lin CF, Lin YT, Bau DT, Tsay GJ, Patel ZM, Tsou YA, Tzankov A, Matter MS, Tai CJ, Yeh TH, Hwang PH, Nolan GP, Nayak JV, Jackson PK. ACE2 localizes to the respiratory cilia and is not increased by ACE inhibitors or ARBs. Nat Commun 2020; 11:5453. [PMID: 33116139 PMCID: PMC7595232 DOI: 10.1038/s41467-020-19145-6] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/30/2020] [Indexed: 12/26/2022] Open
Abstract
The coronavirus SARS-CoV-2 is the causative agent of the ongoing severe acute respiratory disease pandemic COVID-19. Tissue and cellular tropism is one key to understanding the pathogenesis of SARS-CoV-2. We investigate the expression and subcellular localization of the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), within the upper (nasal) and lower (pulmonary) respiratory tracts of human donors using a diverse panel of banked tissues. Here, we report our discovery that the ACE2 receptor protein robustly localizes within the motile cilia of airway epithelial cells, which likely represents the initial or early subcellular site of SARS-CoV-2 viral entry during host respiratory transmission. We further determine whether ciliary ACE2 expression in the upper airway is influenced by patient demographics, clinical characteristics, comorbidities, or medication use, and show the first mechanistic evidence that the use of angiotensin-converting enzyme inhibitors (ACEI) or angiotensin II receptor blockers (ARBs) does not increase susceptibility to SARS-CoV-2 infection through enhancing the expression of ciliary ACE2 receptor. These findings are crucial to our understanding of the transmission of SARS-CoV-2 for prevention and control of this virulent pathogen.
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Affiliation(s)
- Ivan T Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Tsuguhisa Nakayama
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Phillip A Gall
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Chun-Kang Liao
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Liang-Chun Shih
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Christian M Schürch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - David R McIlwain
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nicole A Borchard
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - David Zarabanda
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Sachi S Dholakia
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela Yang
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Dayoung Kim
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chia-Der Lin
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Ming-Hsui Tsai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Katie M Phillips
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Raymond Kim
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan B Overdevest
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, Columbia University School of Medicine, New York City, NY, USA
| | - Matthew A Tyler
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Carol H Yan
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Chih-Feng Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Tsen Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Da-Tian Bau
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Gregory J Tsay
- School of Medicine, China Medical University, Taichung, Taiwan
- Division of Immunology and Rheumatology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Zara M Patel
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Yung-An Tsou
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Matthias S Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Chih-Jaan Tai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Te-Huei Yeh
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Peter H Hwang
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter K Jackson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
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26
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Kelly MR, Kostyrko K, Han K, Mooney NA, Jeng EE, Spees K, Dinh PT, Abbott KL, Gwinn DM, Sweet-Cordero EA, Bassik MC, Jackson PK. Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities. Cancer Discov 2020; 10:1950-1967. [PMID: 32727735 PMCID: PMC7710624 DOI: 10.1158/2159-8290.cd-19-1274] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 06/08/2020] [Accepted: 07/24/2020] [Indexed: 11/16/2022]
Abstract
Activating mutations in RAS GTPases drive many cancers, but limited understanding of less-studied RAS interactors, and of the specific roles of different RAS interactor paralogs, continues to limit target discovery. We developed a multistage discovery and screening process to systematically identify genes conferring RAS-related susceptibilities in lung adenocarcinoma. Using affinity purification mass spectrometry, we generated a protein-protein interaction map of RAS interactors and pathway components containing hundreds of interactions. From this network, we constructed a CRISPR dual knockout library targeting 119 RAS-related genes that we screened for KRAS-dependent genetic interactions (GI). This approach identified new RAS effectors, including the adhesion controller RADIL and the endocytosis regulator RIN1, and >250 synthetic lethal GIs, including a potent KRAS-dependent interaction between RAP1GDS1 and RHOA. Many GIs link specific paralogs within and between gene families. These findings illustrate the power of multiomic approaches to uncover synthetic lethal combinations specific for hitherto untreatable cancer genotypes. SIGNIFICANCE: We establish a deep network of protein-protein and genetic interactions in the RAS pathway. Many interactions validated here demonstrate important specificities and redundancies among paralogous RAS regulators and effectors. By comparing synthetic lethal interactions across KRAS-dependent and KRAS-independent cell lines, we identify several new combination therapy targets for RAS-driven cancers.This article is highlighted in the In This Issue feature, p. 1775.
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Affiliation(s)
- Marcus R Kelly
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California.,Program in Cancer Biology, Stanford University School of Medicine, Stanford, California
| | - Kaja Kostyrko
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Kyuho Han
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California
| | - Edwin E Jeng
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Kaitlyn Spees
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Phuong T Dinh
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Keene L Abbott
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California
| | - Dana M Gwinn
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - E Alejandro Sweet-Cordero
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California.
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, California. .,Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California. .,Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
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27
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Coles GL, Cristea S, Webber JT, Levin RS, Moss SM, He A, Sangodkar J, Hwang YC, Arand J, Drainas AP, Mooney NA, Demeter J, Spradlin JN, Mauch B, Le V, Shue YT, Ko JH, Lee MC, Kong C, Nomura DK, Ohlmeyer M, Swaney DL, Krogan NJ, Jackson PK, Narla G, Gordan JD, Shokat KM, Sage J. Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells. Cancer Cell 2020; 38:129-143.e7. [PMID: 32531271 PMCID: PMC7363571 DOI: 10.1016/j.ccell.2020.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 02/18/2020] [Accepted: 05/04/2020] [Indexed: 12/23/2022]
Abstract
Using unbiased kinase profiling, we identified protein kinase A (PKA) as an active kinase in small cell lung cancer (SCLC). Inhibition of PKA activity genetically, or pharmacologically by activation of the PP2A phosphatase, suppresses SCLC expansion in culture and in vivo. Conversely, GNAS (G-protein α subunit), a PKA activator that is genetically activated in a small subset of human SCLC, promotes SCLC development. Phosphoproteomic analyses identified many PKA substrates and mechanisms of action. In particular, PKA activity is required for the propagation of SCLC stem cells in transplantation studies. Broad proteomic analysis of recalcitrant cancers has the potential to uncover targetable signaling networks, such as the GNAS/PKA/PP2A axis in SCLC.
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Affiliation(s)
- Garry L Coles
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sandra Cristea
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - James T Webber
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rebecca S Levin
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Steven M Moss
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Andy He
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jaya Sangodkar
- Division of Genetic Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yeonjoo C Hwang
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julia Arand
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brandon Mauch
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Vicky Le
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yan Ting Shue
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julie H Ko
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Myung Chang Lee
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Christina Kong
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Ohlmeyer
- Icahn School of Medicine at Mount Sinai, New York, NY, USA; Atux Iskay LLC, Plainsboro, New Jersey, NJ 08536, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; David J. Gladstone Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; David J. Gladstone Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Peter K Jackson
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Goutham Narla
- Division of Genetic Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John D Gordan
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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28
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Lee IT, Nakayama T, Wu CT, Goltsev Y, Jiang S, Gall PA, Liao CK, Shih LC, Schürch CM, McIlwain DR, Chu P, Borchard NA, Zarabanda D, Dholakia SS, Yang A, Kim D, Kanie T, Lin CD, Tsai MH, Phillips KM, Kim R, Overdevest JB, Tyler MA, Yan CH, Lin CF, Lin YT, Bau DT, Tsay GJ, Patel ZM, Tsou YA, Tai CJ, Yeh TH, Hwang PH, Nolan GP, Nayak JV, Jackson PK. Robust ACE2 protein expression localizes to the motile cilia of the respiratory tract epithelia and is not increased by ACE inhibitors or angiotensin receptor blockers. medRxiv 2020:2020.05.08.20092866. [PMID: 32511516 PMCID: PMC7273284 DOI: 10.1101/2020.05.08.20092866] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We investigated the expression and subcellular localization of the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), within the upper (nasal) and lower (pulmonary) respiratory tracts of healthy human donors. We detected ACE2 protein expression within the cilia organelle of ciliated airway epithelial cells, which likely represents the initial or early subcellular site of SARS-CoV-2 viral entry during respiratory transmission. We further determined whether ACE2 expression in the cilia of upper respiratory cells was influenced by patient demographics, clinical characteristics, co-morbidities, or medication use, and found no evidence that the use of angiotensin-converting enzyme inhibitors (ACEI) or angiotensin II receptor blockers (ARBs) increases ACE2 protein expression.
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Affiliation(s)
- Ivan T. Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally: Ivan T. Lee, Tsuguhisa Nakayama, Chien-Ting Wu, Yury Goltsev
| | - Tsuguhisa Nakayama
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- These authors contributed equally: Ivan T. Lee, Tsuguhisa Nakayama, Chien-Ting Wu, Yury Goltsev
| | - Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
- These authors contributed equally: Ivan T. Lee, Tsuguhisa Nakayama, Chien-Ting Wu, Yury Goltsev
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- These authors contributed equally: Ivan T. Lee, Tsuguhisa Nakayama, Chien-Ting Wu, Yury Goltsev
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Phillip A. Gall
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Chun-Kang Liao
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Liang-Chun Shih
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Christian M. Schürch
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - David R. McIlwain
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Nicole A. Borchard
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - David Zarabanda
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Sachi S. Dholakia
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Angela Yang
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Dayoung Kim
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Chia-Der Lin
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Ming-Hsui Tsai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Katie M. Phillips
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Raymond Kim
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Jonathan B. Overdevest
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otolaryngology–Head and Neck Surgery, Columbia University School of Medicine, New York City, NY
| | - Matthew A. Tyler
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otolaryngology–Head and Neck Surgery, University of Minnesota School of Medicine, Minneapolis, MN
| | - Carol H. Yan
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otolaryngology–Head and Neck Surgery, University of California San Diego School of Medicine, San Diego, CA
| | - Chih-Feng Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Tsen Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Da-Tian Bau
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Gregory J. Tsay
- School of Medicine, China Medical University, Taichung, Taiwan
- Division of Immunology and Rheumatology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Zara M. Patel
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Yung-An Tsou
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Chih-Jaan Tai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Te-Huei Yeh
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Peter H. Hwang
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Garry P. Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- These authors jointly supervised this work: Garry P. Nolan, Jayakar V. Nayak, Peter K. Jackson
| | - Jayakar V. Nayak
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- These authors jointly supervised this work: Garry P. Nolan, Jayakar V. Nayak, Peter K. Jackson
| | - Peter K. Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
- These authors jointly supervised this work: Garry P. Nolan, Jayakar V. Nayak, Peter K. Jackson
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29
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Kelly M, Han K, Kostyrko K, Mooney N, Jeng E, Demeter J, Sweet-Cordero A, Bassik M, Jackson PK. Abstract B25: Combined proteomic and genetic interaction mapping reveals new Ras pathway effectors and regulators. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-b25] [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
Despite intensive study, no drugs in clinical use specifically target KRAS-mutant tumors. Uncharacterized feedback pathways and unmapped compensatory pathways, including compensation among paralogs, hinder our ability to target Ras effector pathways, requiring a better catalogue of pathways upstream and downstream of Ras. We used tandem affinity purification of Kras, Hras and Nras, their activated alleles and key proteins with known regulatory (GEFs, GAPs) or effectors (Raf, RalGDS1, RIN1/2) in both 293 cells and A549 NSCLC cells to generate a high-confidence protein-protein interaction (PPI) network of 220 proteins showing 1,400 physical interactions. The network was used to design an sgRNA library (10 sgRNAs/gene) and screen Cas9-expressing A549 cells for strong growth dependencies. These data were then used to select 120 genes and construct a 2-gene tandem sgRNA library of highest relevance to the Ras pathway (with 60 control sgRNAs). This 2-gene sgRNA library was tested in A549 and H23 NSCLC lines for quantitative single and two gene-dependent quantitative changes in growth, showing 100s of strong synthetic lethals among 14K pairwise tests. These genetic interactions in conjunction with PPIs and TCGA data identify extensive coupling between Raf/MEK/ERK kinases, Ral and Rap GTPases, the Rap1GDS1 small GTPase controller, and RADIL cell adhesion pathways. The screen identified new candidate effector pathways for cell adhesion, Rap GTPase regulation, and protein processing, including new understudied Kras direct effectors RADIL, RGL1/2/3, and RIN1/2. Additional 20 x 20 custom libraries were screened in a broader panel of Kras-mutant versus other NSCLC lines. These screens revealed systematic Kras-dependent synthetic lethality among components of the MAP kinase pathway (ERK1/ERK2, ERK1/RAF1, MEK1/MEK2 etc.) and other interactions between the MAPK pathway and components of the Ral and Rap GTPase, RADIL cell adhesion pathways and RIN1-dependent macropinocytosis pathways. Using the recent Kras G12C inhibitor in H23 cells, we have validated that sgRNA knockouts of these Kras effector affect these specific, new pathways: cell adhesion via RADIL, growth signaling via Rap1GDS1 and RhoA, and macropinocytosis via the Rab5 GEF RIN1. Application of the Kras inhibitor ARS-853 shows much-reduced effects on specific Kras effector pathways in cells deleted for these specific effectors, showing these effectors are highly coupled to Kras. Our systematic data reveal new genetic vulnerabilities and target candidates with potential for new therapeutics.
Citation Format: Marcus Kelly, Kyuho Han, Kaja Kostyrko, Nancie Mooney, Edwin Jeng, Janos Demeter, Alejandro Sweet-Cordero, Michael Bassik, Peter K. Jackson. Combined proteomic and genetic interaction mapping reveals new Ras pathway effectors and regulators [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B25.
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Affiliation(s)
| | | | - Kaja Kostyrko
- 2University of California San Francisco, San Francisco, CA
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30
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Bennett HW, Gustavsson AK, Bayas CA, Petrov PN, Mooney N, Moerner WE, Jackson PK. Novel fibrillar structure in the inversin compartment of primary cilia revealed by 3D single-molecule superresolution microscopy. Mol Biol Cell 2020; 31:619-639. [PMID: 31895004 PMCID: PMC7202064 DOI: 10.1091/mbc.e19-09-0499] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary cilia in many cell types contain a periaxonemal subcompartment called the inversin compartment. Four proteins have been found to assemble within the inversin compartment: INVS, ANKS6, NEK8, and NPHP3. The function of the inversin compartment is unknown, but it appears to be critical for normal development, including left–right asymmetry and renal tissue homeostasis. Here we combine superresolution imaging of human RPE1 cells, a classic model for studying primary cilia in vitro, with a genetic dissection of the protein–protein binding relationships that organize compartment assembly to develop a new structural model. We observe that INVS is the core structural determinant of a compartment composed of novel fibril-like substructures, which we identify here by three-dimensional single-molecule superresolution imaging. We find that NEK8 and ANKS6 depend on INVS for localization to these fibrillar assemblies and that ANKS6-NEK8 density within the compartment is regulated by NEK8. Together, NEK8 and ANKS6 are required downstream of INVS to localize and concentrate NPHP3 within the compartment. In the absence of these upstream components, NPHP3 is redistributed within cilia. These results provide a more detailed structure for the inversin compartment and introduce a new example of a membraneless compartment organized by protein–protein interactions.
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Affiliation(s)
- Henrietta W Bennett
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Anna-Karin Gustavsson
- Department of Chemistry, Stanford University, Stanford, CA 94305.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE 17177, Sweden
| | - Camille A Bayas
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Petar N Petrov
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nancie Mooney
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
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Hilgendorf KI, Johnson CT, Mezger A, Rice SL, Norris AM, Demeter J, Greenleaf WJ, Reiter JF, Kopinke D, Jackson PK. Omega-3 Fatty Acids Activate Ciliary FFAR4 to Control Adipogenesis. Cell 2019; 179:1289-1305.e21. [PMID: 31761534 DOI: 10.1016/j.cell.2019.11.005] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/23/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
Abstract
Adult mesenchymal stem cells, including preadipocytes, possess a cellular sensory organelle called the primary cilium. Ciliated preadipocytes abundantly populate perivascular compartments in fat and are activated by a high-fat diet. Here, we sought to understand whether preadipocytes use their cilia to sense and respond to external cues to remodel white adipose tissue. Abolishing preadipocyte cilia in mice severely impairs white adipose tissue expansion. We discover that TULP3-dependent ciliary localization of the omega-3 fatty acid receptor FFAR4/GPR120 promotes adipogenesis. FFAR4 agonists and ω-3 fatty acids, but not saturated fatty acids, trigger mitosis and adipogenesis by rapidly activating cAMP production inside cilia. Ciliary cAMP activates EPAC signaling, CTCF-dependent chromatin remodeling, and transcriptional activation of PPARγ and CEBPα to initiate adipogenesis. We propose that dietary ω-3 fatty acids selectively drive expansion of adipocyte numbers to produce new fat cells and store saturated fatty acids, enabling homeostasis of healthy fat tissue.
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Affiliation(s)
- Keren I Hilgendorf
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carl T Johnson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stem Cell and Regenerative Medicine Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anja Mezger
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Selena L Rice
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Alessandra M Norris
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Daniel Kopinke
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Hsu J, Arand J, Chaikovsky A, Mooney NA, Demeter J, Brison CM, Oliverio R, Vogel H, Rubin SM, Jackson PK, Sage J. E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family. Nat Commun 2019; 10:2939. [PMID: 31270324 PMCID: PMC6610666 DOI: 10.1038/s41467-019-10901-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/06/2019] [Indexed: 01/22/2023] Open
Abstract
E2F transcription factors are central regulators of cell division and cell fate decisions. E2F4 often represents the predominant E2F activity in cells. E2F4 is a transcriptional repressor implicated in cell cycle arrest and whose repressive activity depends on its interaction with members of the RB family. Here we show that E2F4 is important for the proliferation and the survival of mouse embryonic stem cells. In these cells, E2F4 acts in part as a transcriptional activator that promotes the expression of cell cycle genes. This role for E2F4 is independent of the RB family. Furthermore, E2F4 functionally interacts with chromatin regulators associated with gene activation and we observed decreased histone acetylation at the promoters of cell cycle genes and E2F targets upon loss of E2F4 in RB family-mutant cells. Taken together, our findings uncover a non-canonical role for E2F4 that provide insights into the biology of rapidly dividing cells. E2F transcription factors are regulators of cell division and cell fate decisions. Here the authors show that E2F4 is important for proliferation and survival of mouse ESCs, independent of the RB family, and that E2F4 interacts with chromatin regulators associated with gene activation.
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Affiliation(s)
- Jenny Hsu
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Julia Arand
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Andrea Chaikovsky
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Caileen M Brison
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Romane Oliverio
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Hannes Vogel
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Pathology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Julien Sage
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA. .,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.
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Lin CH, Wang Z, Duque-Afonso J, Wong SHK, Demeter J, Loktev AV, Somervaille TCP, Jackson PK, Cleary ML. Oligomeric self-association contributes to E2A-PBX1-mediated oncogenesis. Sci Rep 2019; 9:4915. [PMID: 30894657 PMCID: PMC6426973 DOI: 10.1038/s41598-019-41393-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 09/23/2018] [Accepted: 03/04/2019] [Indexed: 11/16/2022] Open
Abstract
The PBX1 homeodomain transcription factor is converted by t(1;19) chromosomal translocations in acute leukemia into the chimeric E2A-PBX1 oncoprotein. Fusion with E2A confers potent transcriptional activation and constitutive nuclear localization, bypassing the need for dimerization with protein partners that normally stabilize and regulate import of PBX1 into the nucleus, but the mechanisms underlying its oncogenic activation are incompletely defined. We demonstrate here that E2A-PBX1 self-associates through the PBX1 PBC-B domain of the chimeric protein to form higher-order oligomers in t(1;19) human leukemia cells, and that this property is required for oncogenic activity. Structural and functional studies indicate that self-association facilitates the binding of E2A-PBX1 to DNA. Mutants unable to self-associate are transformation defective, however their oncogenic activity is rescued by the synthetic oligomerization domain of FKBP, which confers conditional transformation properties on E2A-PBX1. In contrast to self-association, PBX1 protein domains that mediate interactions with HOX DNA-binding partners are dispensable. These studies suggest that oligomeric self-association may compensate for the inability of monomeric E2A-PBX1 to stably bind DNA and circumvents protein interactions that otherwise modulate PBX1 stability, nuclear localization, DNA binding, and transcriptional activity. The unique dependence on self-association for E2A-PBX1 oncogenic activity suggests potential approaches for mechanism-based targeted therapies.
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MESH Headings
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Basic Helix-Loop-Helix Transcription Factors/metabolism
- Carcinogenesis/genetics
- Cell Line, Tumor
- Chromosomes, Human, Pair 1/chemistry
- Chromosomes, Human, Pair 19/chemistry
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Pre-B-Cell Leukemia Transcription Factor 1/genetics
- Pre-B-Cell Leukemia Transcription Factor 1/metabolism
- Protein Binding
- Protein Multimerization
- Protein Stability
- Tacrolimus Binding Proteins/genetics
- Tacrolimus Binding Proteins/metabolism
- Transcription, Genetic
- Translocation, Genetic
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Affiliation(s)
- Chiou-Hong Lin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhong Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, 510006, China
| | - Jesús Duque-Afonso
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Hematology and Oncology, University Medical Center Freiburg, Freiburg, Germany
| | - Stephen Hon-Kit Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Janos Demeter
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alexander V Loktev
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tim C P Somervaille
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4GJ, UK
| | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michael L Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Kelly MR, Han K, Mooney N, Jeng E, Kostyrko K, Sweet-Cordero A, Bassik M, Jackson PK. Abstract PR12: A combined protein-protein interaction and genetic interaction map defines new and critical Kras effectors in non-small cell lung cancer. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-pr12] [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
Despite intensive study, no drugs in clinical use specifically target KRAS-mutant tumors. Uncharacterized feedback mechanisms and parallel pathways have stymied the treatment of KRAS-mutant tumors with Raf and PI3K inhibitors, and the KRas protein itself does not easily accommodate binding of small-molecule inhibitors. These challenges demand more systematic and quantitative characterization of the physical and genetic relationships between Ras regulators and effectors.
To that end, we used tandem affinity purification of Kras, Hras and Nras, their activated alleles and key proteins with known regulatory (GEFs, GAPs) or effector (Raf, RalGDS, RIN1/2) roles in both 293 cells and A549 NSCLC cells to generate a high-confidence protein-protein interaction (PPI) network. This map of 220 proteins and 1,400 physical interactions was used to design an sgRNA library with 10 guides/gene. This library was screened in Cas9-expressing A549 cells and grown for 14 days before analysis for dropout or enhanced representation of sgRNAs. Approximately 120 genes showed positive or negative growth effects. PPIs and genetic interactions (GIs) were cross-referenced with public PPI data and TCGA patient data to assemble a combined physical PPI and genetic map informed by cancer mutations. This map suggests many hypotheses for PPIs critical for growth control. This set was used to construct a sgRNA library covering 120 genes of probable relevance to the Ras pathway with ~60 “safe harbor” control sgRNAs. This library was screened in a two-cassette sgRNA system testing 14K pairwise genetic effects to identify quantitative changes in growth in A549 and H23 NSCLC lines. This screen showed >100 genetic interactions, which in conjunction with PPIs, identify coupling between the Raf/MEK/ERK kinase, Ral and Rap GTPase, RNA processing, and cell adhesion pathways. The screen identified new candidate effector pathways for cell adhesion, RNA processing, Rap GTPase regulation, and protein processing, including the RADIL, RGL, and RIN Kras effectors. Validation focused using the synthetic lethal interactions observed in the sgRNA screen to predict drug combinations showing drug synergy in A549 and H23 cells. Using 11-point dose titrations and isobologram analysis of drug combinations, we see strong synergy among PI3 kinase, Raf, and Erk inhibitors in these cells. Using the recently described Kras G12C inhibitor, expressed in H23 cells, we have validated that sgRNA deletion of the the key Kras effector for specific pathways including cell adhesion (RADIL), growth signaling (RAF), and endocytosis/ macropinocytosis (RIN) are affected and that use of the Kras inhibitor ARS-853 shows much reduced effects on specific Kras effector pathways in cells deleted for these effectors. These systematic data underscore the limitations of our current understanding of Kras-driven cancers, revealing new genetic vulnerabilities and target candidates.
This abstract is also being presented as Poster A28.
Citation Format: Marcus R. Kelly, Kyuho Han, Nancie Mooney, Edwin Jeng, Kaja Kostyrko, Alejandro Sweet-Cordero, Michael Bassik, Peter K. Jackson. A combined protein-protein interaction and genetic interaction map defines new and critical Kras effectors in non-small cell lung cancer [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 PR12.
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Affiliation(s)
| | - Kyuho Han
- 1Stanford University School of Medicine, Stanford, CA,
| | - Nancie Mooney
- 1Stanford University School of Medicine, Stanford, CA,
| | - Edwin Jeng
- 1Stanford University School of Medicine, Stanford, CA,
| | - Kaja Kostyrko
- 2University of California San Francisco, San Francisco, CA
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Abstract
EZH2 is frequently amplified in human melanomas. In this issue of Cancer Cell, Zingg et al. find that EZH2 overexpression silences genes for the primary cilium, causing deciliation, Wnt pathway activation, and progression of BrafV600E- or NrasQ61N-driven melanomas, thus defining a tumor-suppressor role for cilia in cancer.
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Affiliation(s)
- Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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36
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Jackson PK. Abstract 1313: A combined protein-protein interaction and genetic interaction map defines new and critical Kras effectors in NSCLC. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1313] [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
Despite intensive study, no drugs in clinical use specifically target KRAS-mutant tumors. Uncharacterized feedback mechanisms and parallel pathways have stymied the treatment of KRAS-mutant tumors with Raf and PI3K inhibitors, and the KRas protein itself does not easily accommodate binding of small-molecule inhibitors. These challenges demand more systematic and quantitative characterization of the physical and genetic relationships between Ras regulators and effectors. Thus we used tandem affinity purification of Kras, Hras and Nras, their activated alleles and key proteins with known regulatory (GEFs, GAPs) or effector (Raf, RalGDS) roles in both 293 cells and A549 NSCLC cells to generate a high-confidence protein-protein interaction (PPI) network. This map of 220 proteins and 1,400 physical interactions was used to design an sgRNA library with 10 guides/gene. This library was screened in Cas9-expressing A549 cells and grown for 14 days before analysis for dropout or enhanced representation of sgRNAs. Approximately 120 genes showed positive or negative growth effects. PPIs and genetic interactions (GIs) were cross-referenced with public PPI data and TCGA patient data to assemble a combined physical PPI and genetic map informed by cancer mutations. This map suggests many hypotheses for PPIs critical for growth control. This set was used to construct a sgRNA library covering 120 genes of probable relevance to the Ras pathway with ~60 “safe harbor” control sgRNAs. This library was screened in a two-cassette sgRNA system testing 14K pairwise genetic effects to identify quantitative changes in growth in A549 and H23 NSCLC lines. This screen showed >100 genetic interactions, which in conjunction with PPIs identify coupling between the Raf/MEK/ERK kinase, Ral and Rap GTPase, RNA processing and cell adhesion pathways. The screen identified new candidate effector pathways for cell adhesion, RNA processing, Rap GTPase regulation and protein processing, including the RADIL, RGL and RIN Kras effectors. Validation focused on using the synthetic lethal interactions observed in the sgRNA screen to predict drug combinations showing drug synergy in A549 and H23 cells. Using 11-point dose titrations and isobologram analysis of drug combinations, we see strong synergy among PI3 kinase, Raf and Erk inhibitors in these cells. Using the recently described Kras G12C inhibitor, expressed in H23 cells, we have validated that sgRNA deletion of the the key Kras effector for specific pathway,s including cell adhesion (RADIL), growth signaling (RAF) and endocytosis/ macropinocytosis (RIN), is affected and that use of the Kras inhibitor ARS-853 shows much-reduced effects on specific Kras effector pathways in cells deleted for these effectors. These systematic data underscore the limitations of our current understanding of Kras-driven cancers, revealing new genetic vulnerabilities and target candidates.
Citation Format: Peter K. Jackson. A combined protein-protein interaction and genetic interaction map defines new and critical Kras effectors in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1313.
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Kostyrko K, Kelly MR, Han K, Jeng EE, Morgens DW, Bassik MC, Jackson PK, Sweet-Cordero A. Abstract 4362: Identification of novel combinatorial synthetic lethal vulnerabilities in KRAS-driven lung cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4362] [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
Lung cancer is the number one cause of cancer-related deaths worldwide. The most prevalent type of lung cancer is Non-Small Cell Lung Cancer (NSCLC). A significant number of patients with NSCLC carry oncogenic KRAS mutations. However, the efforts to target KRAS directly have thus far proven unsuccessful and tumors harboring mutations in this gene remain the most difficult to treat, highlighting the need for alternative approaches. One promising strategy is to target KRAS-dependent cancers through synthetic lethality. However, KRAS activates multiple effector pathways, suggesting that targeting one gene may not be sufficient to fully inhibit KRAS oncogenesis. Therefore, we propose that targeting combinations of genes that together are synthetic lethal with KRAS may constitute a better therapeutic strategy. Furthermore, we hypothesize that a targeted approach focused on the protein-protein interaction network proximal to KRAS may be more effective than the current emphasis on genome-wide screens. To discover novel, combinatorial KRAS synthetic lethal genes, we used affinity purification/mass spectrometry (AP/MS), to systematically identify KRAS interacting proteins and construct a detailed map of protein-protein interactions centered on KRAS. Based on this network we designed a CRISPR/Cas9 library targeting pairwise combinations of KRAS-interacting genes. Using this library we simultaneously knocked-out pairs of 119 genes in two KRAS-driven non-small cell lung cancer (NSCLC) cell lines (A549 and H23). Knock-out of many gene pairs synergistically impaired growth of these cells, while the knock-out of each of the genes alone had no or little effect. We chose 20 most promising targets for further screening in vitro and in vivo in a panel of 9 KRAS-mutant and KRAS wild type Cas9-expressing NSCLC cell lines. We also selected six gene pairs that had the most synergistic effect on growth in A549 and H23 cells for individual validation in Cas9-expressing NSCLC cell lines and normal human bronchial epithelial cells (HBECs). We found that the simultaneous knock-out of one pair of genes, Rap1GDS1 and RhoA, significantly decreased growth of KRAS-dependent NSCLC cells, while having a limited effect on KRAS-independent cells or HBECs. Moreover the knock-out of either of these genes alone had no effect on growth in any of the cell lines, suggesting that only the combination of these two genes is synthetically lethal with KRAS. We are currently performing further validation in organoid cultures and in vivo. Additional validation and human relevance will be determined using patient-derived xenografts (PDX).
Citation Format: Kaja Kostyrko, Marcus R. Kelly, Kyuho Han, Edwin E. Jeng, David W. Morgens, Michael C. Bassik, Peter K. Jackson, Alejandro Sweet-Cordero. Identification of novel combinatorial synthetic lethal vulnerabilities in KRAS-driven lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4362.
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Abstract
GTPases are molecular switches that cycle between the inactive GDP-bound state and the active GTP-bound state. GTPases exchange nucleotides either by its intrinsic nucleotide exchange or by interaction with guanine nucleotide exchange factors (GEFs). Monitoring the nucleotide exchange in vitro, together with reconstitution of direct interactions with regulatory proteins, provides key insights into how a GTPase is activated. In this protocol, we describe core methods to monitor nucleotide exchange using fluorescent N-Methylanthraniloyl (MANT)-guanine nucleotide.
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Affiliation(s)
- Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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39
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Kelly MR, Kyuho H, Jeng EE, Morgans D, Kostyrko K, Simpson D, Gwinn D, Sweet-Cordero A, Bassik MC, Jackson PK. Abstract PR03: Linking AP/MS-driven protein-protein interaction networks and combination CRISPR/sgRNA screens defines new Kras effectors and target candidates for non-small cell lung cancer. Mol Cancer Ther 2017. [DOI: 10.1158/1538-8514.synthleth-pr03] [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
The Kras pathway is a central driver in prevalent and deadly cancers including pancreas, colon and lung. Despite decades of work studying the Raf and PI3 kinase pathways downstream of Kras, therapies targeted to these pathways have shown varied responses in tumors
To better understand whether important Kras dependences have been overlooked, we used tandem affinity purification of Kras, Hras, and Nras interactors and a set of baits representing ~50 interacting pathway regulators, and have compared these interactions in Kras transformed A549 NSCLC lines versus an isogenic shRNA Kras knockdown line, to identify key protein-protein interactions (PPIs) linked to Kras effector activity. These interactions were curated and compared to public PPI, genetic susceptibility, and other multiomics data to assemble a physical PPI map annotated with important functional determinants. This functional map was used to construct a library of 114 selected sgRNAs (10 guides per gene) and screened in a 1140 x 1140 dual sgRNA vector system to look for quantitative changes in single and dual genetic dependencies in A549 cell growth. We discovered a considerable number of new KRAS GTP-specific effectors important in NSCLC cancer, many with strong mutations patterns supported by TCGA data and validated by in vitro biochemical assay. We will present these data and additional validation studies on two pathways including the Radil-Rap1-Kif14 pathway for cell migration and an extensive interaction of the Kras pathway with Ral and Rap GTPase family guanine nucleotide exchange factors. These new effectors underscore limitations in our functional understanding of transformation in Kras-driven tumors and suggest specific new targets for these critical tumors.
Citation Format: Marcus R. Kelly, Han Kyuho, Edwin E. Jeng, David Morgans, Kaja Kostyrko, David Simpson, Dana Gwinn, Alejandro Sweet-Cordero, Michael C. Bassik, Peter K. Jackson. Linking AP/MS-driven protein-protein interaction networks and combination CRISPR/sgRNA screens defines new Kras effectors and target candidates for non-small cell lung cancer [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR03.
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Affiliation(s)
| | - Han Kyuho
- Stanford University School of Medicine, Stanford, CA
| | - Edwin E. Jeng
- Stanford University School of Medicine, Stanford, CA
| | - David Morgans
- Stanford University School of Medicine, Stanford, CA
| | - Kaja Kostyrko
- Stanford University School of Medicine, Stanford, CA
| | - David Simpson
- Stanford University School of Medicine, Stanford, CA
| | - Dana Gwinn
- Stanford University School of Medicine, Stanford, CA
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40
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Qin EY, Cooper DD, Abbott KL, Lennon J, Nagaraja S, Mackay A, Jones C, Vogel H, Jackson PK, Monje M. Neural Precursor-Derived Pleiotrophin Mediates Subventricular Zone Invasion by Glioma. Cell 2017; 170:845-859.e19. [PMID: 28823557 PMCID: PMC5587159 DOI: 10.1016/j.cell.2017.07.016] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 06/15/2017] [Accepted: 07/13/2017] [Indexed: 12/26/2022]
Abstract
The lateral ventricle subventricular zone (SVZ) is a frequent and consequential site of pediatric and adult glioma spread, but the cellular and molecular mechanisms mediating this are poorly understood. We demonstrate that neural precursor cell (NPC):glioma cell communication underpins this propensity of glioma to colonize the SVZ through secretion of chemoattractant signals toward which glioma cells home. Biochemical, proteomic, and functional analyses of SVZ NPC-secreted factors revealed the neurite outgrowth-promoting factor pleiotrophin, along with required binding partners SPARC/SPARCL1 and HSP90B, as key mediators of this chemoattractant effect. Pleiotrophin expression is strongly enriched in the SVZ, and pleiotrophin knock down starkly reduced glioma invasion of the SVZ in the murine brain. Pleiotrophin, in complex with the binding partners, activated glioma Rho/ROCK signaling, and ROCK inhibition decreased invasion toward SVZ NPC-secreted factors. These findings demonstrate a pathogenic role for NPC:glioma interactions and potential therapeutic targets to limit glioma invasion. PAPERCLIP.
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Affiliation(s)
- Elizabeth Y Qin
- Department of Neurology, Stanford University, Palo Alto, CA 94305, USA
| | | | - Keene L Abbott
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University, Palo Alto, CA 94305, USA
| | - James Lennon
- Department of Neurology, Stanford University, Palo Alto, CA 94305, USA
| | - Surya Nagaraja
- Department of Neurology, Stanford University, Palo Alto, CA 94305, USA
| | - Alan Mackay
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Chris Jones
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Hannes Vogel
- Department of Neurology, Stanford University, Palo Alto, CA 94305, USA; Department of Pathology, Stanford University, Palo Alto, CA 94305, USA; Department of Neurosurgery, Stanford University, Palo Alto, CA 94305, USA; Department of Pediatrics, Stanford University, Palo Alto, CA 94305, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University, Palo Alto, CA 94305, USA; Department of Pathology, Stanford University, Palo Alto, CA 94305, USA
| | - Michelle Monje
- Department of Neurology, Stanford University, Palo Alto, CA 94305, USA; Department of Pathology, Stanford University, Palo Alto, CA 94305, USA; Department of Neurosurgery, Stanford University, Palo Alto, CA 94305, USA; Department of Pediatrics, Stanford University, Palo Alto, CA 94305, USA.
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41
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Ding S, Mooney N, Li B, Kelly MR, Feng N, Loktev AV, Sen A, Patton JT, Jackson PK, Greenberg HB. Comparative Proteomics Reveals Strain-Specific β-TrCP Degradation via Rotavirus NSP1 Hijacking a Host Cullin-3-Rbx1 Complex. PLoS Pathog 2016; 12:e1005929. [PMID: 27706223 PMCID: PMC5051689 DOI: 10.1371/journal.ppat.1005929] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [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: 04/22/2016] [Accepted: 09/10/2016] [Indexed: 11/18/2022] Open
Abstract
Rotaviruses (RVs) are the leading cause of severe gastroenteritis in young children, accounting for half a million deaths annually worldwide. RV encodes non-structural protein 1 (NSP1), a well-characterized interferon (IFN) antagonist, which facilitates virus replication by mediating the degradation of host antiviral factors including IRF3 and β-TrCP. Here, we utilized six human and animal RV NSP1s as baits and performed tandem-affinity purification coupled with high-resolution mass spectrometry to comprehensively characterize NSP1-host protein interaction network. Multiple Cullin-RING ubiquitin ligase (CRL) complexes were identified. Importantly, inhibition of cullin-3 (Cul3) or RING-box protein 1 (Rbx1), by siRNA silencing or chemical perturbation, significantly impairs strain-specific NSP1-mediated β-TrCP degradation. Mechanistically, we demonstrate that NSP1 localizes to the Golgi with the host Cul3-Rbx1 CRL complex, which targets β-TrCP and NSP1 for co-destruction at the proteasome. Our study uncovers a novel mechanism that RV employs to promote β-TrCP turnover and provides molecular insights into virus-mediated innate immunity inhibition.
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Affiliation(s)
- Siyuan Ding
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Nancie Mooney
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Bin Li
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Marcus R. Kelly
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ningguo Feng
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Alexander V. Loktev
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Adrish Sen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - John T. Patton
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Peter K. Jackson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Harry B. Greenberg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, California, United States of America
- * E-mail:
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Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ, Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB. The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery. Nat Genet 2016; 48:648-56. [PMID: 27158779 PMCID: PMC4978421 DOI: 10.1038/ng.3558] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/01/2016] [Indexed: 12/21/2022]
Abstract
Cilia use microtubule-based intraflagellar transport (IFT) to organize intercellular signaling. Ciliopathies are a spectrum of human diseases resulting from defects in cilia structure or function. The mechanisms regulating the assembly of ciliary multiprotein complexes and the transport of these complexes to the base of cilia remain largely unknown. Combining proteomics, in vivo imaging and genetic analysis of proteins linked to planar cell polarity (Inturned, Fuzzy and Wdpcp), we identified and characterized a new genetic module, which we term CPLANE (ciliogenesis and planar polarity effector), and an extensive associated protein network. CPLANE proteins physically and functionally interact with the poorly understood ciliopathy-associated protein Jbts17 at basal bodies, where they act to recruit a specific subset of IFT-A proteins. In the absence of CPLANE, defective IFT-A particles enter the axoneme and IFT-B trafficking is severely perturbed. Accordingly, mutation of CPLANE genes elicits specific ciliopathy phenotypes in mouse models and is associated with ciliopathies in human patients.
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Affiliation(s)
- Michinori Toriyama
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - S Paige Taylor
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA.,Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Ivan Duran
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA.,Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Daniel H Cohn
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA
| | - Ange-Line Bruel
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, Dijon, France
| | - Jacqueline M Tabler
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Kevin Drew
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Marcus R Kelly
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Sukyoung Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Tae Joo Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Daniela A Braun
- Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Armand Biver
- Pediatric Unit, Hospital Center, Luxemburg, Luxembourg
| | - Kerstin Wagner
- Cardiological Pediatric Unit, Hospital Center, Luxemburg, Luxembourg
| | - Anne Malfroot
- Clinic of Pediatric Respiratory Diseases, Universitair Ziekenhuis Brussel, Brussels, Belgium.,Infectious Diseases, Travel Clinic, Universitair Ziekenhuis Brussel, Brussels, Belgium.,Cystic Fibrosis Clinic, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Inusha Panigrahi
- Department of Pediatrics Advanced, Pediatric Centre Pigmer, Chandigarh, India
| | - Brunella Franco
- Division of Pediatrics, Department of Medical Translational Sciences, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Hadeel Adel Al-Lami
- Department of Craniofacial and Stem Cell Biology, Dental Institute, King's College London, London, UK
| | - Yvonne Yeung
- Department of Craniofacial and Stem Cell Biology, Dental Institute, King's College London, London, UK
| | - Yeon Ja Choi
- Department of Pathology, Stony Brook University, Stony Brook, New York, USA.,Department of Dermatology, Stony Brook University, Stony Brook, New York, USA
| | | | - Yannis Duffourd
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, Dijon, France
| | - Laurence Faivre
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, Dijon, France.,Clinical Genetics Centre, FHU-TRANSLAD, Children Hospital, CHU Dijon, Dijon, France.,Eastern Referral Centre for Developmental Anomalies and Malformative Syndromes, FHU-TRANSLAD, Children Hospital, CHU Dijon, Dijon, France
| | - Jean-Baptiste Rivière
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, Dijon, France.,Laboratory of Molecular Genetics, FHU-TRANSLAD, PTB, CHU Dijon, Dijon, France
| | - Jiang Chen
- Department of Pathology, Stony Brook University, Stony Brook, New York, USA.,Department of Dermatology, Stony Brook University, Stony Brook, New York, USA
| | - Karen J Liu
- Department of Craniofacial and Stem Cell Biology, Dental Institute, King's College London, London, UK
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Friedhelm Hildebrandt
- Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Christel Thauvin-Robinet
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, Dijon, France.,Laboratory of Molecular Genetics, FHU-TRANSLAD, PTB, CHU Dijon, Dijon, France
| | - Deborah Krakow
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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Affiliation(s)
- Dominic P Norris
- Mammalian Genetics Unit, MRC Harwell, Harwell Campus OX11 0RD, UK
| | - Peter K Jackson
- Departments of Microbiology &Immunology and Pathology, and in the Baxter Laboratory, Stanford University School of Medicine, Stanford, California 94305, USA
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Pal K, Hwang SH, Somatilaka B, Badgandi H, Jackson PK, DeFea K, Mukhopadhyay S. Smoothened determines β-arrestin-mediated removal of the G protein-coupled receptor Gpr161 from the primary cilium. J Cell Biol 2016; 212:861-75. [PMID: 27002170 PMCID: PMC4810300 DOI: 10.1083/jcb.201506132] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/11/2016] [Indexed: 02/08/2023] Open
Abstract
Dynamic changes in membrane protein composition of the primary cilium are central to development and homeostasis, but we know little about mechanisms regulating membrane protein flux. Stimulation of the sonic hedgehog (Shh) pathway in vertebrates results in accumulation and activation of the effector Smoothened within cilia and concomitant disappearance of a negative regulator, the orphan G protein-coupled receptor (GPCR), Gpr161. Here, we describe a two-step process determining removal of Gpr161 from cilia. The first step involves β-arrestin recruitment by the signaling competent receptor, which is facilitated by the GPCR kinase Grk2. An essential factor here is the ciliary trafficking and activation of Smoothened, which by increasing Gpr161-β-arrestin binding promotes Gpr161 removal, both during resting conditions and upon Shh pathway activation. The second step involves clathrin-mediated endocytosis, which functions outside of the ciliary compartment in coordinating Gpr161 removal. Mechanisms determining dynamic compartmentalization of Gpr161 in cilia define a new paradigm for down-regulation of GPCRs during developmental signaling from a specialized subcellular compartment.
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Affiliation(s)
- Kasturi Pal
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Bandarigoda Somatilaka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Hemant Badgandi
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Peter K Jackson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Kathryn DeFea
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA 92521
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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Abstract
The mysteriously diverse phenotypes in mice lacking the p53 homolog p73 are recently unified by new analysis showing p73 is required for formation of multiciliated epithelia. p73 directly activates FoxJ1, the central transcriptional driver for multiciliation, and induces a host of genes critical for ciliogenesis.
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Affiliation(s)
- Peter K Jackson
- Stanford University School of Medicine, Baxter Laboratory, Departments of Microbiology and Immunology and Pathology, Stanford, CA 94305, USA.
| | - Laura D Attardi
- Stanford University School of Medicine, Department of Radiation Oncology and Department of Genetics, Stanford, CA 94305, USA
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Hilgendorf KI, Johnson CT, Jackson PK. The primary cilium as a cellular receiver: organizing ciliary GPCR signaling. Curr Opin Cell Biol 2016; 39:84-92. [PMID: 26926036 DOI: 10.1016/j.ceb.2016.02.008] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 12/12/2022]
Abstract
The primary cilium is an antenna-like cellular protrusion mediating sensory and neuroendocrine signaling. Its localization within tissue architecture and a growing list of cilia-localized receptors, in particular G-protein-coupled receptors, determine a host of crucial physiologies, which are disrupted in human ciliopathies. Here, we discuss recent advances in the identification and characterization of ciliary signaling components and pathways. Recent studies have highlighted the unique signaling environment of the primary cilium and we are just beginning to understand how this design allows for highly amplified and regulated signaling.
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Affiliation(s)
- Keren I Hilgendorf
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carl T Johnson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stem Cell and Regenerative Medicine PhD Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Acharya S, Petersen KY, Golubkov V, Kwong M, Adams CM, Jackson PK, Lewis DB. Abstract 5002: Abstract Submission. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-5002] [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
Protein tyrosine kinase 7 (PTK7), a catalytically inactive receptor tyrosine kinase (RTK) that is highly expressed by T-lineage cells during intrathymic development, is a novel marker for human CD4+ recent thymic emigrants (RTEs), and is also highly expressed on some T-lineage thymomas, e.g., Jurkat cells as well as inprimary T-Acute Lymphoblastic leukemia. The function of PTK7 in normal human T-cell development and in oncogenesis remains unclear. Here, using RNAi-mediated gene silencing in T-lineage tumor cells, primary human peripheral T-cells, and thymocytes, we found that targeting PTK7 consistently decreased cell survival by augmenting caspase-3 activation of apoptosis. The PTK7 knockdown also decreased AKT phosphorylation and PI3 kinase activity, suggesting an essential role for PTK7 in survival of RTEs and developing thymocytes involving the PI3K/AKT pathway. Using mass spectrometry we identified insulin-like growth factor-1 (IGF-1) receptor as an active kinase partner of PTK7. This interaction was biologically relevant in that PTK7 downregulation also reduced IGF-1R-dependent survival signals in T-lineage cells. As enhanced IGF-1-dependent signaling is a frequent event in oncogenesis, the intersection of PTK7 with the IGF-1 signaling pathway suggests the potential of PTK7-directed therapy of T-lineage tumors.
Citation Format: Swati Acharya, Kira Y.D Petersen, Vladislav Golubkov, Mandy Kwong, Christopher M. Adams, Peter K. Jackson, David B. Lewis. Abstract Submission. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5002. doi:10.1158/1538-7445.AM2015-5002
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Affiliation(s)
- Swati Acharya
- 1Stanford University School of Medicine, Stanford, CA
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48
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Lu Q, Insinna C, Ott C, Stauffer J, Pintado PA, Rahajeng J, Baxa U, Walia V, Cuenca A, Hwang YS, Daar IO, Lopes S, Lippincott-Schwartz J, Jackson PK, Caplan S, Westlake CJ. Erratum: Early steps in primary cilium assembly require EHD1/EHD3-dependent ciliary vesicle formation. Nat Cell Biol 2015; 17:531. [DOI: 10.1038/ncb3155] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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49
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Gholkar AA, Senese S, Lo YC, Capri J, Deardorff WJ, Dharmarajan H, Contreras E, Hodara E, Whitelegge JP, Jackson PK, Torres JZ. Tctex1d2 associates with short-rib polydactyly syndrome proteins and is required for ciliogenesis. Cell Cycle 2015; 14:1116-25. [PMID: 25830415 PMCID: PMC4614626 DOI: 10.4161/15384101.2014.985066] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/28/2014] [Accepted: 11/03/2014] [Indexed: 12/26/2022] Open
Abstract
Short-rib polydactyly syndromes (SRPS) arise from mutations in genes involved in retrograde intraflagellar transport (IFT) and basal body homeostasis, which are critical for cilia assembly and function. Recently, mutations in WDR34 or WDR60 (candidate dynein intermediate chains) were identified in SRPS. We have identified and characterized Tctex1d2, which associates with Wdr34, Wdr60 and other dynein complex 1 and 2 subunits. Tctex1d2 and Wdr60 localize to the base of the cilium and their depletion causes defects in ciliogenesis. We propose that Tctex1d2 is a novel dynein light chain important for trafficking to the cilium and potentially retrograde IFT and is a new molecular link to understanding SRPS pathology.
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Affiliation(s)
- Ankur A. Gholkar
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Silvia Senese
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Yu-Chen Lo
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
- Program in Bioengineering; University of California; Los Angeles, CA USA
| | - Joseph Capri
- Pasarow Mass Spectrometry Laboratory; The Jane and Terry Semel Institute for Neuroscience and Human Behavior; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - William J Deardorff
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Harish Dharmarajan
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Ely Contreras
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Emmanuelle Hodara
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory; The Jane and Terry Semel Institute for Neuroscience and Human Behavior; David Geffen School of Medicine; University of California; Los Angeles, CA USA
- Molecular Biology Institute; University of California; Los Angeles, CA USA
| | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology; Department of Microbiology & Immunology; Stanford University School of Medicine; Stanford, CA USA
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
- Molecular Biology Institute; University of California; Los Angeles, CA USA
- Jonsson Comprehensive Cancer Center; University of California; Los Angeles, CA USA
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50
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Beales P, Jackson PK. Acknowledgement of Cilia’s reviewers in 2013. Cilia 2014. [PMCID: PMC3899740 DOI: 10.1186/2046-2530-3-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Contributing reviewers
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