1
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Sherman DJ, Liu L, Mamrosh JL, Xie J, Ferbas J, Lomenick B, Ladinsky MS, Verma R, Rulifson IC, Deshaies RJ. The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics. Proc Natl Acad Sci U S A 2024; 121:e2318619121. [PMID: 38657050 PMCID: PMC11067037 DOI: 10.1073/pnas.2318619121] [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: 10/25/2023] [Accepted: 03/16/2024] [Indexed: 04/26/2024] Open
Abstract
Nonalcoholic fatty liver disease, recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3, encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD. Despite its discovery 20 y ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-driven cellular change.
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Affiliation(s)
| | - Lei Liu
- Amgen Research, South San Francisco, CA94080
| | | | | | | | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Mark S. Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
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2
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Gu L, Li M, Li CM, Haratipour P, Lingeman R, Jossart J, Gutova M, Flores L, Hyde C, Kenjić N, Li H, Chung V, Li H, Lomenick B, Von Hoff DD, Synold TW, Aboody KS, Liu Y, Horne D, Hickey RJ, Perry JJP, Malkas LH. Small molecule targeting of transcription-replication conflict for selective chemotherapy. Cell Chem Biol 2023; 30:1235-1247.e6. [PMID: 37531956 PMCID: PMC10592352 DOI: 10.1016/j.chembiol.2023.07.001] [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: 05/12/2022] [Revised: 02/12/2023] [Accepted: 07/10/2023] [Indexed: 08/04/2023]
Abstract
Targeting transcription replication conflicts, a major source of endogenous DNA double-stranded breaks and genomic instability could have important anticancer therapeutic implications. Proliferating cell nuclear antigen (PCNA) is critical to DNA replication and repair processes. Through a rational drug design approach, we identified a small molecule PCNA inhibitor, AOH1996, which selectively kills cancer cells. AOH1996 enhances the interaction between PCNA and the largest subunit of RNA polymerase II, RPB1, and dissociates PCNA from actively transcribed chromatin regions, while inducing DNA double-stranded breaks in a transcription-dependent manner. Attenuation of RPB1 interaction with PCNA, by a point mutation in RPB1's PCNA-binding region, confers resistance to AOH1996. Orally administrable and metabolically stable, AOH1996 suppresses tumor growth as a monotherapy or as a combination treatment but causes no discernable side effects. Inhibitors of transcription replication conflict resolution may provide a new and unique therapeutic avenue for exploiting this cancer-selective vulnerability.
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Affiliation(s)
- Long Gu
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| | - Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Caroline M Li
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Pouya Haratipour
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Robert Lingeman
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jennifer Jossart
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Margarita Gutova
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda Flores
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Caitlyn Hyde
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Nikola Kenjić
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA
| | - Haiqing Li
- Department of Genomics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Vincent Chung
- Department of Medical Oncology, City of Hope, Duarte, CA, USA
| | - Hongzhi Li
- Department of Bioinformatics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Daniel D Von Hoff
- Clinical Translational Research Division, Translational Genomics Research Institute, 445N 5th Street, Phoenix, AZ 85004, USA
| | - Timothy W Synold
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Karen S Aboody
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - David Horne
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Robert J Hickey
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - J Jefferson P Perry
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda H Malkas
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
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3
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Sherman DJ, Liu L, Mamrosh JL, Xie J, Ferbas J, Lomenick B, Ladinsky MS, Verma R, Rulifson IC, Deshaies RJ. The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics. bioRxiv 2023:2023.10.13.562302. [PMID: 37873239 PMCID: PMC10592801 DOI: 10.1101/2023.10.13.562302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3, encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD to date. Despite its discovery twenty years ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-driven cellular change.
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Affiliation(s)
| | - Lei Liu
- Amgen Research, South San Francisco, CA 94080, USA
| | | | | | - John Ferbas
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark S. Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rati Verma
- Amgen Research, Thousand Oaks, CA 91320, USA
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4
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Mohanty A, Nam A, Srivastava S, Jones J, Lomenick B, Singhal SS, Guo L, Cho H, Li A, Behal A, Mirzapoiazova T, Massarelli E, Koczywas M, Arvanitis LD, Walser T, Villaflor V, Hamilton S, Mambetsariev I, Sattler M, Nasser MW, Jain M, Batra SK, Soldi R, Sharma S, Fakih M, Mohanty SK, Mainan A, Wu X, Chen Y, He Y, Chou TF, Roy S, Orban J, Kulkarni P, Salgia R. Acquired resistance to KRAS G12C small-molecule inhibitors via genetic/nongenetic mechanisms in lung cancer. Sci Adv 2023; 9:eade3816. [PMID: 37831779 PMCID: PMC10575592 DOI: 10.1126/sciadv.ade3816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
Inherent or acquired resistance to sotorasib poses a substantialt challenge for NSCLC treatment. Here, we demonstrate that acquired resistance to sotorasib in isogenic cells correlated with increased expression of integrin β4 (ITGB4), a component of the focal adhesion complex. Silencing ITGB4 in tolerant cells improved sotorasib sensitivity, while overexpressing ITGB4 enhanced tolerance to sotorasib by supporting AKT-mTOR bypass signaling. Chronic treatment with sotorasib induced WNT expression and activated the WNT/β-catenin signaling pathway. Thus, silencing both ITGB4 and β-catenin significantly improved sotorasib sensitivity in tolerant, acquired, and inherently resistant cells. In addition, the proteasome inhibitor carfilzomib (CFZ) exhibited synergism with sotorasib by down-regulating ITGB4 and β-catenin expression. Furthermore, adagrasib phenocopies the combination effect of sotorasib and CFZ by suppressing KRAS activity and inhibiting cell cycle progression in inherently resistant cells. Overall, our findings unveil previously unrecognized nongenetic mechanisms underlying resistance to sotorasib and propose a promising treatment strategy to overcome resistance.
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Affiliation(s)
- Atish Mohanty
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Arin Nam
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Saumya Srivastava
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Jeff Jones
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sharad S. Singhal
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Linlin Guo
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Hyejin Cho
- Integrative Genomics Core, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Aimin Li
- Department of Pathology, City of Hope National Medical Center, Duarte, CA 91010,USA
| | - Amita Behal
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Tamara Mirzapoiazova
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Erminia Massarelli
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Marianna Koczywas
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | | | - Tonya Walser
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Victoria Villaflor
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Stanley Hamilton
- Department of Pathology, City of Hope National Medical Center, Duarte, CA 91010,USA
| | - Isa Mambetsariev
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mohd W. Nasser
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Maneesh Jain
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Surinder K. Batra
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Raffaella Soldi
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, AZ 850043, USA
| | - Sunil Sharma
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, AZ 850043, USA
| | - Marwan Fakih
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Saswat Kumar Mohanty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Avijit Mainan
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Yihong Chen
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Yanan He
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - John Orban
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Prakash Kulkarni
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Ravi Salgia
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
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5
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Ninova M, Holmes H, Lomenick B, Fejes Tóth K, Aravin AA. Pervasive SUMOylation of heterochromatin and piRNA pathway proteins. Cell Genom 2023; 3:100329. [PMID: 37492097 PMCID: PMC10363806 DOI: 10.1016/j.xgen.2023.100329] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 07/27/2023]
Abstract
Genome regulation involves complex protein interactions that are often mediated through post-translational modifications (PTMs). SUMOylation-modification by the small ubiquitin-like modifier (SUMO)-has been implicated in numerous essential processes in eukaryotes. In Drosophila, SUMO is required for viability and fertility, with its depletion from ovaries leading to heterochromatin loss and ectopic transposon and gene activation. Here, we developed a proteomics-based strategy to uncover the Drosophila ovarian "SUMOylome," which revealed that SUMOylation is widespread among proteins involved in heterochromatin regulation and different aspects of the Piwi-interacting small RNA (piRNA) pathway that represses transposons. Furthermore, we show that SUMOylation of several piRNA pathway proteins occurs in a Piwi-dependent manner. Together, these data highlight broad implications of protein SUMOylation in epigenetic regulation and indicate novel roles of this modification in the cellular defense against genomic parasites. Finally, this work provides a resource for the study of SUMOylation in other biological contexts in the Drosophila model.
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Affiliation(s)
- Maria Ninova
- Department of Biochemistry, University of California Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, USA
| | - Hannah Holmes
- Department of Biochemistry, University of California Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory of the Beckman Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Alexei A. Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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6
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Mamrosh JL, Sherman DJ, Cohen JR, Johnston JA, Joubert MK, Li J, Lipford JR, Lomenick B, Moradian A, Prabhu S, Sweredoski MJ, Vander Lugt B, Verma R, Deshaies RJ. Quantitative measurement of the requirement of diverse protein degradation pathways in MHC class I peptide presentation. Sci Adv 2023; 9:eade7890. [PMID: 37352349 PMCID: PMC10289651 DOI: 10.1126/sciadv.ade7890] [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] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/17/2023] [Indexed: 06/25/2023]
Abstract
Peptides from degradation of intracellular proteins are continuously displayed by major histocompatibility complex (MHC) class I. To better understand origins of these peptides, we performed a comprehensive census of the class I peptide repertoire in the presence and absence of ubiquitin-proteasome system (UPS) activity upon developing optimized methodology to enrich for and quantify these peptides. Whereas most class I peptides are dependent on the UPS for their generation, a surprising 30%, enriched in peptides of mitochondrial origin, appears independent of the UPS. A further ~10% of peptides were found to be dependent on the proteasome but independent of ubiquitination for their generation. Notably, clinically achievable partial inhibition of the proteasome resulted in display of atypical peptides. Our results suggest that generation of MHC class I•peptide complexes is more complex than previously recognized, with UPS-dependent and UPS-independent components; paradoxically, alternative protein degradation pathways also generate class I peptides when canonical pathways are impaired.
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Affiliation(s)
- Jennifer L. Mamrosh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - David J. Sherman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - Joseph R. Cohen
- Process Development, Amgen Inc., Thousand Oaks, CA 91320, USA
| | | | | | - Jing Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | | | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Michael J. Sweredoski
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Rati Verma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - Raymond J. Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
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7
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Griffin ME, Thompson JW, Xiao Y, Sweredoski MJ, Aksenfeld RB, Jensen EH, Koldobskaya Y, Schacht AL, Kim TD, Choudhry P, Lomenick B, Garbis SD, Moradian A, Hsieh-Wilson LC. Functional glycoproteomics by integrated network assembly and partitioning. bioRxiv 2023:2023.06.13.541482. [PMID: 37398272 PMCID: PMC10312638 DOI: 10.1101/2023.06.13.541482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The post-translational modification (PTM) of proteins by O-linked β-N-acetyl-D-glucosamine (O-GlcNAcylation) is widespread across the proteome during the lifespan of all multicellular organisms. However, nearly all functional studies have focused on individual protein modifications, overlooking the multitude of simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here, we describe Networking of Interactors and SubstratEs (NISE), a novel, systems-level approach to rapidly and comprehensively monitor O-GlcNAcylation across the proteome. Our method integrates affinity purification-mass spectrometry (AP-MS) and site-specific chemoproteomic technologies with network generation and unsupervised partitioning to connect potential upstream regulators with downstream targets of O-GlcNAcylation. The resulting network provides a data-rich framework that reveals both conserved activities of O-GlcNAcylation such as epigenetic regulation as well as tissue-specific functions like synaptic morphology. Beyond O-GlcNAc, this holistic and unbiased systems-level approach provides a broadly applicable framework to study PTMs and discover their diverse roles in specific cell types and biological states.
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Affiliation(s)
- Matthew E. Griffin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Co-first author
| | - John W. Thompson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Co-first author
| | - Yao Xiao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Co-first author
| | - Michael J. Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rita B. Aksenfeld
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elizabeth H. Jensen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yelena Koldobskaya
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew L. Schacht
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Terry D. Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Priya Choudhry
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Spiros D. Garbis
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Linda C. Hsieh-Wilson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Lead contact
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8
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Jones J, MacKrell EJ, Wang TY, Lomenick B, Roukes ML, Chou TF. Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization. BMC Bioinformatics 2023; 24:239. [PMID: 37280522 DOI: 10.1186/s12859-023-05360-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND The analysis of mass spectrometry-based quantitative proteomics data can be challenging given the variety of established analysis platforms, the differences in reporting formats, and a general lack of approachable standardized post-processing analyses such as sample group statistics, quantitative variation and even data filtering. We developed tidyproteomics to facilitate basic analysis, improve data interoperability and potentially ease the integration of new processing algorithms, mainly through the use of a simplified data-object. RESULTS The R package tidyproteomics was developed as both a framework for standardizing quantitative proteomics data and a platform for analysis workflows, containing discrete functions that can be connected end-to-end, thus making it easier to define complex analyses by breaking them into small stepwise units. Additionally, as with any analysis workflow, choices made during analysis can have large impacts on the results and as such, tidyproteomics allows researchers to string each function together in any order, select from a variety of options and in some cases develop and incorporate custom algorithms. CONCLUSIONS Tidyproteomics aims to simplify data exploration from multiple platforms, provide control over individual functions and analysis order, and serve as a tool to assemble complex repeatable processing workflows in a logical flow. Datasets in tidyproteomics are easy to work with, have a structure that allows for biological annotations to be added, and come with a framework for developing additional analysis tools. The consistent data structure and accessible analysis and plotting tools also offers a way for researchers to save time on mundane data manipulation tasks.
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Affiliation(s)
- Jeff Jones
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.
| | - Elliot J MacKrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Ting-Yu Wang
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Michael L Roukes
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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9
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Wang GZ, Warren EA, Haas AL, Peña AS, Kiedrowski MR, Lomenick B, Chou TF, Bomberger JM, Tirrell DA, Limoli DH. Staphylococcal secreted cytotoxins are competition sensing signals for Pseudomonas aeruginosa. bioRxiv 2023:2023.01.29.526047. [PMID: 36747623 PMCID: PMC9900984 DOI: 10.1101/2023.01.29.526047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Coinfection with two notorious opportunistic pathogens, the Gram-negative Pseudomonas aeruginosa and Gram-positive Staphylococcus aureus , dominates chronic pulmonary infections. While coinfection is associated with poor patient outcomes, the interspecies interactions responsible for such decline remain unknown. Here, we dissected molecular mechanisms of interspecies sensing between P. aeruginosa and S. aureus . We discovered that P. aeruginosa senses S. aureus secreted peptides and, counterintuitively, moves towards these toxins. P. aeruginosa tolerates such a strategy through "competition sensing", whereby it preempts imminent danger/competition by arming cells with type six secretion (T6S) and iron acquisition systems. Intriguingly, while T6S is predominantly described as weaponry targeting Gram-negative and eukaryotic cells, we find that T6S is essential for full P. aeruginosa competition with S. aureus , a previously undescribed role for T6S. Importantly, competition sensing was activated during coinfection of bronchial epithelia, including T6S islands targeting human cells. This study reveals critical insight into both interspecies competition and how antagonism may cause collateral damage to the host environment.
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10
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Guna A, Stevens TA, Inglis AJ, Replogle JM, Esantsi TK, Muthukumar G, Shaffer KCL, Wang ML, Pogson AN, Jones JJ, Lomenick B, Chou TF, Weissman JS, Voorhees RM. MTCH2 is a mitochondrial outer membrane protein insertase. Science 2022; 378:317-322. [PMID: 36264797 PMCID: PMC9674023 DOI: 10.1126/science.add1856] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [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] [Indexed: 11/23/2022]
Abstract
In the mitochondrial outer membrane, α-helical transmembrane proteins play critical roles in cytoplasmic-mitochondrial communication. Using genome-wide CRISPR screens, we identified MTCH2, and its paralog MTCH1, and showed that it is required for insertion of biophysically diverse tail-anchored (TA), signal-anchored, and multipass proteins, but not outer membrane β-barrel proteins. Purified MTCH2 was sufficient to mediate insertion into reconstituted proteoliposomes. Functional and mutational studies suggested that MTCH2 has evolved from a solute carrier transporter. MTCH2 uses membrane-embedded hydrophilic residues to function as a gatekeeper for the outer membrane, controlling mislocalization of TAs into the endoplasmic reticulum and modulating the sensitivity of leukemia cells to apoptosis. Our identification of MTCH2 as an insertase provided a mechanistic explanation for the diverse phenotypes and disease states associated with MTCH2 dysfunction. We showed that MTCH2 was both necessary and sufficient for insertion of diverse α-helical proteins into the mitochondrial outer membrane, and was the defining member of a family of insertases that have co-opted the SLC25 transporter fold.
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Affiliation(s)
- Alina Guna
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kelly C L Shaffer
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Maxine L Wang
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Angela N Pogson
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jeff J Jones
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
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11
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Spero MA, Jones J, Lomenick B, Chou TF, Newman DK. Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa. Mol Microbiol 2022; 118:321-335. [PMID: 36271736 PMCID: PMC9589919 DOI: 10.1111/mmi.14972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/25/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that often encounters hypoxic/anoxic environments within the host, which increases its tolerance to many conventional antibiotics. Toward identifying novel treatments, we explored the therapeutic potential of chlorate, a pro-drug that kills hypoxic/anoxic, antibiotic-tolerant P. aeruginosa populations. While chlorate itself is relatively nontoxic, it is enzymatically reduced to the toxic oxidizing agent, chlorite, by hypoxically induced nitrate reductase. To better assess chlorate's therapeutic potential, we investigated mechanisms of chlorate toxicity and resistance in P. aeruginosa. We used transposon mutagenesis to identify genes that alter P. aeruginosa fitness during chlorate treatment, finding that methionine sulfoxide reductases (Msr), which repair oxidized methionine residues, support survival during chlorate stress. Chlorate treatment leads to proteome-wide methionine oxidation, which is exacerbated in a ∆msrA∆msrB strain. In response to chlorate, P. aeruginosa upregulates proteins involved in a wide range of functions, including metabolism, DNA replication/repair, protein repair, transcription, and translation, and these newly synthesized proteins are particularly vulnerable to methionine oxidation. The addition of exogenous methionine partially rescues P. aeruginosa survival during chlorate treatment, suggesting that widespread methionine oxidation contributes to death. Finally, we found that mutations that decrease nitrate reductase activity are a common mechanism of chlorate resistance.
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Affiliation(s)
- Melanie A. Spero
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Jeff Jones
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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12
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Ravanfar R, Sheng Y, Shahgholi M, Lomenick B, Jones J, Chou TF, Gray HB, Winkler JR. Surface cysteines could protect the SARS-CoV-2 main protease from oxidative damage. J Inorg Biochem 2022; 234:111886. [PMID: 35675741 PMCID: PMC9161685 DOI: 10.1016/j.jinorgbio.2022.111886] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/28/2022] [Accepted: 05/29/2022] [Indexed: 11/19/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is responsible for cleaving twelve nonstructural proteins from the viral polyprotein. Mpro, a cysteine protease, is characterized by a large number of noncatalytic cysteine (Cys) residues, none involved in disulfide bonds. In the absence of a tertiary-structure stabilizing role for these residues, a possible alternative is that they are involved in redox processes. We report experimental work in support of a proposal that surface cysteines on Mpro can protect the active-site Cys145 from oxidation by reactive oxygen species (ROS). In investigations of enzyme kinetics, we found that mutating three surface cysteines to serines did not greatly affect activity, which in turn indicates that these cysteines could protect Cys145 from oxidative damage.
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Affiliation(s)
- Raheleh Ravanfar
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Yuling Sheng
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Mona Shahgholi
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jeff Jones
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Harry B Gray
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
| | - Jay R Winkler
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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13
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Yang CI, Zhu Z, Jones JJ, Lomenick B, Chou TF, Shan SO. System-wide analyses reveal essential roles of N-terminal protein modification in bacterial membrane integrity. iScience 2022; 25:104756. [PMID: 35942092 PMCID: PMC9356101 DOI: 10.1016/j.isci.2022.104756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/20/2022] [Accepted: 07/07/2022] [Indexed: 11/18/2022] Open
Abstract
The removal of the N-terminal formyl group on nascent proteins by peptide deformylase (PDF) is the most prevalent protein modification in bacteria. PDF is a critical target of antibiotic development; however, its role in bacterial physiology remains a long-standing question. This work used the time-resolved analyses of the Escherichia coli translatome and proteome to investigate the consequences of PDF inhibition. Loss of PDF activity rapidly induces cellular stress responses, especially those associated with protein misfolding and membrane defects, followed by a global down-regulation of metabolic pathways. Rapid membrane hyperpolarization and impaired membrane integrity were observed shortly after PDF inhibition, suggesting that the plasma membrane disruption is the most immediate and primary consequence of formyl group retention on nascent proteins. This work resolves the physiological function of a ubiquitous protein modification and uncovers its crucial role in maintaining the structure and function of the bacterial membrane. PDF inhibition induces membrane defects and metabolic imbalance Deformylation is involved in nascent protein folding Membrane is the earliest and primary target of N-formylation on nascent proteins PDF activity is essential for redox homeostasis in bacteria
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Affiliation(s)
- Chien-I Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zikun Zhu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jeffrey J. Jones
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Corresponding author
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14
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Cheng YS, Zhang T, Ma X, Pratuangtham S, Zhang GC, Ondrus AA, Mafi A, Lomenick B, Jones JJ, Ondrus AE. A proteome-wide map of 20(S)-hydroxycholesterol interactors in cell membranes. Nat Chem Biol 2021; 17:1271-1280. [PMID: 34799735 PMCID: PMC8607797 DOI: 10.1038/s41589-021-00907-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 02/19/2021] [Accepted: 09/25/2021] [Indexed: 12/28/2022]
Abstract
Oxysterols (OHCs) are hydroxylated cholesterol metabolites that play ubiquitous roles in health and disease. Due to the non-covalent nature of their interactions and their unique partitioning in membranes, the analysis of live-cell, proteome-wide interactions of OHCs remains an unmet challenge. Here, we present a structurally precise chemoproteomics probe for the biologically active molecule 20(S)-hydroxycholesterol (20(S)-OHC) and provide a map of its proteome-wide targets in the membranes of living cells. Our target catalog consolidates diverse OHC ontologies and demonstrates that OHC-interacting proteins cluster with specific processes in immune response and cancer. Competition experiments reveal that 20(S)-OHC is a chemo-, regio- and stereoselective ligand for the protein transmembrane protein 97 (Tmem97/the σ2 receptor), enabling us to reconstruct the 20(S)-OHC-Tmem97 binding site. Our results demonstrate that multiplexed, quantitative analysis of cellular target engagement can expose new dimensions of metabolite activity and identify actionable targets for molecular therapy.
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Affiliation(s)
- Yu-Shiuan Cheng
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tianyi Zhang
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xiang Ma
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sarida Pratuangtham
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grace C Zhang
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alexander A Ondrus
- Mathematics Department, Northern Alberta Institute of Technology, Edmonton, Alberta, Canada
| | - Amirhossein Mafi
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Jeffrey J Jones
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Alison E Ondrus
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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15
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Spero M, Jones J, Lomenick B, Zareian S, Chou T, Newman D. 428: Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)01852-x] [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] [Indexed: 11/28/2022]
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16
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Wang F, Moen DR, Sauni C, Kan SH, Li S, Le SQ, Lomenick B, Zhang X, Ekins S, Singamsetty S, Wood J, Dickson PI, Chou TF. Enzyme Replacement Therapy for Mucopolysaccharidosis IIID using Recombinant Human α- N-Acetylglucosamine-6-Sulfatase in Neonatal Mice. Mol Pharm 2020; 18:214-227. [PMID: 33320673 DOI: 10.1021/acs.molpharmaceut.0c00831] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There is currently no cure or effective treatment available for mucopolysaccharidosis type IIID (MPS IIID, Sanfilippo syndrome type D), a lysosomal storage disorder (LSD) caused by the deficiency of α-N-acetylglucosamine-6-sulfatase (GNS). The clinical symptoms of MPS IIID, like other subtypes of Sanfilippo syndrome, are largely localized to the central nervous system (CNS), and any treatments aiming to ameliorate or reverse the catastrophic and fatal neurologic decline caused by this disease need to be delivered across the blood-brain barrier. Here, we report a proof-of-concept enzyme replacement therapy (ERT) for MPS IIID using recombinant human α-N-acetylglucosamine-6-sulfatase (rhGNS) via intracerebroventricular (ICV) delivery in a neonatal MPS IIID mouse model. We overexpressed and purified rhGNS from CHO cells with a specific activity of 3.9 × 104 units/mg protein and a maximal enzymatic activity at lysosomal pH (pH 5.6), which was stable for over one month at 4 °C in artificial cerebrospinal fluid (CSF). We demonstrated that rhGNS was taken up by MPS IIID patient fibroblasts via the mannose 6-phosphate (M6P) receptor and reduced intracellular glycosaminoglycans to normal levels. The delivery of 5 μg of rhGNS into the lateral cerebral ventricle of neonatal MPS IIID mice resulted in normalization of the enzymatic activity in brain tissues; rhGNS was found to be enriched in lysosomes in MPS IIID-treated mice relative to the control. Furthermore, a single dose of rhGNS was able to reduce the accumulated heparan sulfate and β-hexosaminidase. Our results demonstrate that rhGNS delivered into CSF is a potential therapeutic option for MPS IIID that is worthy of further development.
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Affiliation(s)
- Feng Wang
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, California 90502, United States.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Derek R Moen
- Phoenix Nest Inc., Brooklyn, New York 11232, United States
| | - Chelsee Sauni
- Phoenix Nest Inc., Brooklyn, New York 11232, United States
| | - Shih-Hsin Kan
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, California 90502, United States.,Research Administration, CHOC Children's Hospital, Orange, California 92868, United States
| | - Shan Li
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, California 90502, United States.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Steven Q Le
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, California 90502, United States.,Department of Pediatrics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Xiaoyi Zhang
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, California 90502, United States
| | - Sean Ekins
- Phoenix Nest Inc., Brooklyn, New York 11232, United States
| | | | - Jill Wood
- Phoenix Nest Inc., Brooklyn, New York 11232, United States
| | - Patricia I Dickson
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, California 90502, United States.,Department of Pediatrics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Tsui-Fen Chou
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center and The Lundquist Institute, Torrance, California 90502, United States.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
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17
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Reubsaet L, Sweredoski MJ, Moradian A, Lomenick B, Eggleston-Rangel R, Garbis SD. Nano volume fractionation strategy for dilute-and-shoot injections in off-line loss-less proteomic workflows for extensive protein identifications of ultra-low sample amounts. J Chromatogr A 2020; 1609:460507. [PMID: 31522804 DOI: 10.1016/j.chroma.2019.460507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/14/2019] [Accepted: 09/02/2019] [Indexed: 11/20/2022]
Abstract
A proteomic workflow for a simple loss-less manual nano-fractionation (300 nL/fraction) for low µg sample amounts which avoids the need to dry down or transfer fractions to autosampler vials is shown to be feasible. It is demonstrated that the conventional procedure of drying samples down followed by reconstitution negatively affects the number of protein and peptide identifications. Furthermore, these losses seem to disproportionately affect hydrophobic peptides from the drying down and reconstitution step. By collecting and concatenating the fractions while the outlet of the column is submerged in a small predefined volume of 0.2% formic acid, the content of acetonitrile in the collecting vials was lowered such that it was compatible with direct injection for the online analysis. This additionally resulted in a time gain of approx. an hour for the total fractionation time. Acetonitrile concentrations up to 7.5% do not seem to compromise the chromatographic performance in the online analysis. Using as little as 2 µg digested HeLa lysate, approx. 7000 protein groups could be easily identified with 2 or more unique peptides. This was the case when fractionation was performed at pH 10 as well as at pH 5.5.
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Affiliation(s)
- Léon Reubsaet
- Department of Pharmacy, University of Oslo, Oslo, Norway; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA.
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Roxana Eggleston-Rangel
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Spiros D Garbis
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
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18
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Young CD, Tatieng S, Kongmanas K, Fongmoon D, Lomenick B, Yoon AJ, Kiattiburut W, Compostella F, Faull KF, Suree N, Angel JB, Tanphaichitr N. Cover. Am J Reprod Immunol 2019. [DOI: 10.1111/aji.13164] [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] [Indexed: 12/01/2022] Open
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19
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Young CD, Tatieng S, Kongmanas K, Fongmoon D, Lomenick B, Yoon AJ, Kiattiburut W, Compostella F, Faull KF, Suree N, Angel JB, Tanphaichitr N. Sperm can act as vectors for HIV-1 transmission into vaginal and cervical epithelial cells. Am J Reprod Immunol 2019; 82:e13129. [PMID: 31066971 DOI: 10.1111/aji.13129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/02/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
PROBLEM Sperm are the major cells in semen. Human sperm possess a number of HIV-1 gp120 binding ligands including sulfogalactosylglycerolipid (SGG). However, the mechanisms of how sperm capture HIV-1 onto their surface are unclear. Furthermore, the ability of sperm to deliver HIV-1 to vaginal/cervical epithelial cells lining the lower female reproductive tract, as a first step in HIV-1 transmission, needs to be determined. METHOD OF STUDY Sperm from healthy donors were incubated with dual-tropic HIV-1CS204 (clinical isolate), and virus capture was determined by p24 antigen ELISA. The involvement of SGG in HIV-1 capture was assessed by determining Kd values of HIV-1 gp120-SGG binding as well as computational docking of SGG to the gp120 V3 loop. The ability of sperm-associated HIV-1 to infect peripheral blood mononuclear cells (PBMCs) and TZM-bl indicator cells was determined. Lastly, infection of vaginal (Vk2/E6E7), ectocervical (Ect1/E6E7), and endocervical (End1/E6E7) epithelial cells mediated by HIV-1-associated sperm was evaluated. RESULTS Sperm were able to capture HIV-1 in a dose-dependent manner, and the capture reached a maximum within 5 minutes. Captured HIV-1, however, could be removed from sperm by Percoll-gradient centrifugation. Affinity of gp120 for SGG was substantial, implicating sperm SGG in HIV-1 capture. Sperm-associated HIV-1 could productively infect PBMCs and TZM-bl cells, and was capable of being transmitted into vaginal/cervical epithelial cells. CONCLUSION Sperm are able to capture HIV-1, which remains infectious and is able to be transmitted into vaginal/cervical epithelial cells, a result indicating the importance of sperm in HIV transmission.
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Affiliation(s)
- Charlene D Young
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Suriya Tatieng
- Multidisciplinary Program in Biotechnology, The Graduate School, Division of Biochemistry and Biochemical Technology, Faculty of Science, Department of Chemistry, Chiang Mai University, Chiang Mai, Thailand
| | - Kessiri Kongmanas
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Duriya Fongmoon
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Brett Lomenick
- Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, Los Angeles, California
| | - Alexander J Yoon
- Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, Los Angeles, California
| | - Wongsakorn Kiattiburut
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Immunology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Federica Compostella
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | - Kym F Faull
- Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, Los Angeles, California
| | - Nuttee Suree
- Multidisciplinary Program in Biotechnology, The Graduate School, Division of Biochemistry and Biochemical Technology, Faculty of Science, Department of Chemistry, Chiang Mai University, Chiang Mai, Thailand
| | - Jonathan B Angel
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.,Division in Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Nongnuj Tanphaichitr
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.,Faculty of Medicine, Department of Obstetrics & Gynecology, University of Ottawa, Ottawa, Ontario, Canada
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20
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Lomenick B, Shi H, Huang J, Chen C. Identification and characterization of β-sitosterol target proteins. Bioorg Med Chem Lett 2015; 25:4976-4979. [PMID: 25804720 DOI: 10.1016/j.bmcl.2015.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 02/28/2015] [Accepted: 03/03/2015] [Indexed: 11/27/2022]
Abstract
β-Sitosterol is the most abundant plant sterol in the human diet. It is also the major component of several traditional medicines, including saw palmetto and devil's claw. Although β-sitosterol is effective against enlarged prostate in human clinical trials and has anti-cancer and anti-inflammatory activities, the mechanisms of action are poorly understood. Here, we report the identification of two new binding proteins for β-sitosterol that may underlie its beneficial effects.
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Affiliation(s)
- Brett Lomenick
- Department of Molecular and Medical Pharmacology, 23-231 Center for Health Sciences, 650 Charles E Young Dr. South, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Heping Shi
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Jing Huang
- Department of Molecular and Medical Pharmacology, 23-231 Center for Health Sciences, 650 Charles E Young Dr. South, University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Chuo Chen
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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21
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Chin RM, Fu X, Pai MY, Vergnes L, Hwang H, Deng G, Diep S, Lomenick B, Meli VS, Monsalve GC, Hu E, Whelan SA, Wang JX, Jung G, Solis GM, Fazlollahi F, Kaweeteerawat C, Quach A, Nili M, Krall AS, Godwin HA, Chang HR, Faull KF, Guo F, Jiang M, Trauger SA, Saghatelian A, Braas D, Christofk HR, Clarke CF, Teitell MA, Petrascheck M, Reue K, Jung ME, Frand AR, Huang J. The metabolite α-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR. Nature 2014; 510:397-401. [PMID: 24828042 DOI: 10.1038/nature13264] [Citation(s) in RCA: 396] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/17/2014] [Indexed: 12/11/2022]
Abstract
Metabolism and ageing are intimately linked. Compared with ad libitum feeding, dietary restriction consistently extends lifespan and delays age-related diseases in evolutionarily diverse organisms. Similar conditions of nutrient limitation and genetic or pharmacological perturbations of nutrient or energy metabolism also have longevity benefits. Recently, several metabolites have been identified that modulate ageing; however, the molecular mechanisms underlying this are largely undefined. Here we show that α-ketoglutarate (α-KG), a tricarboxylic acid cycle intermediate, extends the lifespan of adult Caenorhabditis elegans. ATP synthase subunit β is identified as a novel binding protein of α-KG using a small-molecule target identification strategy termed drug affinity responsive target stability (DARTS). The ATP synthase, also known as complex V of the mitochondrial electron transport chain, is the main cellular energy-generating machinery and is highly conserved throughout evolution. Although complete loss of mitochondrial function is detrimental, partial suppression of the electron transport chain has been shown to extend C. elegans lifespan. We show that α-KG inhibits ATP synthase and, similar to ATP synthase knockdown, inhibition by α-KG leads to reduced ATP content, decreased oxygen consumption, and increased autophagy in both C. elegans and mammalian cells. We provide evidence that the lifespan increase by α-KG requires ATP synthase subunit β and is dependent on target of rapamycin (TOR) downstream. Endogenous α-KG levels are increased on starvation and α-KG does not extend the lifespan of dietary-restricted animals, indicating that α-KG is a key metabolite that mediates longevity by dietary restriction. Our analyses uncover new molecular links between a common metabolite, a universal cellular energy generator and dietary restriction in the regulation of organismal lifespan, thus suggesting new strategies for the prevention and treatment of ageing and age-related diseases.
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Affiliation(s)
- Randall M Chin
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Xudong Fu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Melody Y Pai
- 1] Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA [2]
| | - Laurent Vergnes
- 1] Department of Human Genetics, University of California Los Angeles, Los Angeles, California 90095, USA [2]
| | - Heejun Hwang
- 1] Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA [2]
| | - Gang Deng
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Simon Diep
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Brett Lomenick
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Vijaykumar S Meli
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Gabriela C Monsalve
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Eileen Hu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Stephen A Whelan
- Department of Surgery, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Jennifer X Wang
- Small Molecule Mass Spectrometry Facility, FAS Division of Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Gwanghyun Jung
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Gregory M Solis
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Farbod Fazlollahi
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Chitrada Kaweeteerawat
- Department of Environmental Health Sciences, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Austin Quach
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Mahta Nili
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Abby S Krall
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Hilary A Godwin
- Department of Environmental Health Sciences, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Helena R Chang
- Department of Surgery, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Kym F Faull
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Feng Guo
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Meisheng Jiang
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Sunia A Trauger
- Small Molecule Mass Spectrometry Facility, FAS Division of Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Daniel Braas
- 1] Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA [2] UCLA Metabolomics Center, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Heather R Christofk
- 1] Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA [2] UCLA Metabolomics Center, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Catherine F Clarke
- 1] Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA [2] Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Michael A Teitell
- 1] Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA [2] Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Michael Petrascheck
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Karen Reue
- 1] Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA [2] Department of Human Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Michael E Jung
- 1] Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA [2] Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Alison R Frand
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Jing Huang
- 1] Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA [2] Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California 90095, USA
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22
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Gao S, Wang Q, Wang G, Lomenick B, Liu J, Fan CW, Deng LW, Huang J, Lum L, Chen C. The Chemistry and Biology of Nakiterpiosin - C-nor-D-Homosteroids. Synlett 2012; 16:2298-2310. [PMID: 23226922 PMCID: PMC3515072 DOI: 10.1055/s-0031-1290460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Isolated from the sponge Terpios hoshinota that causes coral black disease, nakiterpiosin was the first C-nor-D-homosteroid discovered from a marine source. We provide in this account an overview of the chemistry and biology of this natural product. We also include a short history of the synthesis of C-nor-D-homosteroids and the results of some unpublished biological studies of nakiterpiosin.
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Affiliation(s)
- Shuanhu Gao
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Qiaoling Wang
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Gelin Wang
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Brett Lomenick
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California 90095, USA
| | - Jie Liu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chih-Wei Fan
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA, Fax +1(214)6480320
| | - Lih-Wen Deng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jing Huang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California 90095, USA
| | - Lawrence Lum
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA, Fax +1(214)6480320
| | - Chuo Chen
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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23
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Abstract
Drug Affinity Responsive Target Stability is a general methodology for identifying and studying protein-ligand interactions. The technique is based on the principle that when a small molecule compound binds to a protein, the interaction stabilizes the target protein's structure such that it becomes protease resistant. DARTS is particularly useful for the initial identification of the protein targets of small molecules, but can also be used to validate potential protein-ligand interactions predicted or identified by other means and to estimate the affinity of interactions. The approach is simple and advantageous because it can be performed using crude cell lysates and other complex protein mixtures (without requiring purified proteins), and uses native, unmodified small molecules. The protocols provided in this article describe the general approach for performing DARTS experiments, which can be easily modified and scaled to fit the criteria and purpose of any individual project.
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Affiliation(s)
- Brett Lomenick
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles
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24
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Aldana-Masangkay GI, Rodriguez-Gonzalez A, Lin T, Ikeda AK, Hsieh YT, Kim YM, Lomenick B, Okemoto K, Landaw EM, Wang D, Mazitschek R, Bradner JE, Sakamoto KM. Tubacin suppresses proliferation and induces apoptosis of acute lymphoblastic leukemia cells. Leuk Lymphoma 2011; 52:1544-55. [PMID: 21699378 DOI: 10.3109/10428194.2011.570821] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Over the past decade, histone deacetylase inhibitors have increasingly been used to treat various malignancies. Tubacin (tubulin acetylation inducer) is a small molecule that inhibits histone deacetylase 6 (HDAC6) and induces acetylation of α-tubulin. We observed a higher antiproliferative effect of tubacin in acute lymphoblastic leukemia (ALL) cells than in normal hematopoietic cells. Treatment with tubacin led to the induction of apoptotic pathways in both pre-B and T cell ALL cells at a 50% inhibitory concentration (IC(50)) of low micromolar concentrations. Acetylation of α-tubulin increases within the first 30 min following treatment of ALL cells with tubacin. We also observed an accumulation of polyubiquitinated proteins and poly(ADP-ribose) polymerase (PARP) cleavage. Furthermore, the signaling pathways activated by tubacin appear to be distinct from those observed in multiple myeloma. In this article, we demonstrate that tubacin enhances the effects of chemotherapy to treat primary ALL cells in vitro and in vivo. These results suggest that targeting HDAC6 alone or in combination with chemotherapy could provide a novel approach to treat ALL.
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Abstract
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Small-molecule target identification is a vital and daunting task for the chemical biology community as well as for researchers interested in applying the power of chemical genetics to impact biology and medicine. To overcome this “target ID” bottleneck, new technologies are being developed that analyze protein–drug interactions, such as drug affinity responsive target stability (DARTS), which aims to discover the direct binding targets (and off targets) of small molecules on a proteome scale without requiring chemical modification of the compound. Here, we review the DARTS method, discuss why it works, and provide new perspectives for future development in this area.
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Affiliation(s)
- Brett Lomenick
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California 90095, United States
| | - Richard W. Olsen
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California 90095, United States
| | - Jing Huang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California 90095, United States
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26
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Aghajan M, Jonai N, Flick K, Fu F, Luo M, Cai X, Ouni I, Pierce N, Tang X, Lomenick B, Damoiseaux R, Hao R, Del Moral PM, Verma R, Li Y, Li C, Houk KN, Jung ME, Zheng N, Huang L, Deshaies RJ, Kaiser P, Huang J. Chemical genetics screen for enhancers of rapamycin identifies a specific inhibitor of an SCF family E3 ubiquitin ligase. Nat Biotechnol 2010; 28:738-42. [PMID: 20581845 PMCID: PMC2902569 DOI: 10.1038/nbt.1645] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [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: 03/09/2010] [Accepted: 05/09/2010] [Indexed: 01/09/2023]
Abstract
The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control1. With prevalent hyper-activation of the mTOR pathway in human cancers2, novel strategies to enhance TOR pathway inhibition are highly desirable. We used a yeast-based platform to identify small-molecule enhancers of rapamycin (SMERs) and discovered an inhibitor of the SCFMet30 ubiquitin ligase (SMER3). The large SCF (Skp1-Cullin-F-box) family of ubiquitin ligases performs important functions in diverse cellular processes including transcription, cell-cycle control, and immune response3. Accordingly, there would be great value in developing SCF ligase inhibitors that act by a defined mechanism to specifically inactivate ligase activity. We show here that SMER3 selectively inhibits SCFMet30 in vivo and in vitro, but not the closely related SCFCdc4. Our results demonstrate that there is no fundamental barrier to obtaining specific inhibitors to modulate function of individual SCF complexes, and suggest new strategies for combination therapy with rapamycin.
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Affiliation(s)
- Mariam Aghajan
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, and the Molecular Biology Institute, University of California, Los Angeles, California, USA
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