1
|
Shirley JD, Nauta KM, Gillingham JR, Diwakar S, Carlson EE. kinact / KI Value Determination for Penicillin-Binding Proteins in Live Cells. bioRxiv 2024:2024.05.05.592586. [PMID: 38746240 PMCID: PMC11092749 DOI: 10.1101/2024.05.05.592586] [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] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Penicillin-binding proteins (PBPs) are an essential family of bacterial enzymes that are inhibited by the β-lactam class of antibiotics. PBP inhibition disrupts cell wall biosynthesis, which results in deficient growth and proliferation, and ultimately leads to lysis. IC 50 values are often employed as descriptors of enzyme inhibition and inhibitor selectivity but can be misleading in the study of time-dependent, irreversible inhibitors. Due to this disconnect, the second order rate constant k inact / K I is a more appropriate metric of covalent inhibitor potency. Despite being the gold standard measurement of potency, k inact / K I values are typically obtained from in vitro assays, which limits assay throughput if investigating an enzyme family with multiple homologs (such as the PBPs). Therefore, we developed a whole-cell k inact / K I assay to define inhibitor potency for the PBPs in Streptococcus pneumoniae using the fluorescent activity-based probe Bocillin-FL. Our results align with in vitro k inact / K I data and show a comparable relationship to previously established IC 50 values. These results support the validity of our in vivo k inact / K I method as a means of obtaining a full picture of β-lactam potency for a suite of PBPs. Abstract Figure
Collapse
|
2
|
Stan DL, Kim JO, Schaid DJ, Carlson EE, Kim CA, Sinnwell JP, Couch FJ, Vachon CM, Cooke AL, Goldenberg BA, Pruthi S. Breast Cancer Polygenic-Risk Score Influence on Risk-Reducing Endocrine Therapy Use: Genetic Risk Estimate (GENRE) Trial 1-Year and 2-Year Follow-Up. Cancer Prev Res (Phila) 2024; 17:77-84. [PMID: 38154464 DOI: 10.1158/1940-6207.capr-23-0256] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/26/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
Refinement of breast cancer risk estimates with a polygenic-risk score (PRS) may improve uptake of risk-reducing endocrine therapy (ET). A previous clinical trial assessed the influence of adding a PRS to traditional risk estimates on ET use. We stratified participants according to PRS-refined breast cancer risk and evaluated ET use and ET-related quality of life (QOL) at 1-year (previously reported) and 2-year follow-ups. Of 151 participants, 58 (38.4%) initiated ET, and 22 (14.6%) discontinued ET by 2 years; 42 (27.8%) and 36 (23.8%) participants were using ET at 1- and 2-year follow-ups, respectively. At the 2-year follow-up, 39% of participants with a lifetime breast cancer risk of 40.1% to 100.0%, 18% with a 20.1% to 40.0% risk, and 16% with a 0.0% to 20.0% risk were taking ET (overall P = 0.01). Moreover, 40% of participants whose breast cancer risk increased by 10% or greater with addition of the PRS to a traditional breast cancer-risk model were taking ET versus 0% whose risk decreased by 10% or greater (P = 0.004). QOL was similar for participants taking or not taking ET at 1- and 2-year follow-ups, although most who discontinued ET did so because of adverse effects. However, these QOL results may have been skewed by the long interval between QOL surveys and lack of baseline QOL data. PRS-informed breast cancer prevention counseling has a lasting, but waning, effect over time. Additional follow-up studies are needed to address the effect of PRS on ET adherence, ET-related QOL, supplemental breast cancer screening, and other risk-reducing behaviors. PREVENTION RELEVANCE Risk-reducing medications for breast cancer are considerably underused. Informing women at risk with precise and individualized risk assessment tools may substantially affect the incidence of breast cancer. In our study, a risk assessment tool (IBIS-polygenic-risk score) yielded promising results, with 39% of women at highest risk starting preventive medication.
Collapse
Affiliation(s)
- Daniela L Stan
- Breast Diagnostic Clinic, Mayo Clinic, Rochester, Minnesota
- Mayo Clinic Cancer Center, Mayo Clinic, Rochester, Minnesota
| | - Julian O Kim
- Department of Radiation Oncology, Max Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Daniel J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Erin E Carlson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Christina A Kim
- Department of Medical Oncology and Hematology, Max Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jason P Sinnwell
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Fergus J Couch
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Andrew L Cooke
- Department of Radiation Oncology, Max Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Benjamin A Goldenberg
- Department of Medical Oncology and Hematology, Max Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sandhya Pruthi
- Breast Diagnostic Clinic, Mayo Clinic, Rochester, Minnesota
- Mayo Clinic Cancer Center, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
3
|
Mitchell SL, Kearns DB, Carlson EE. Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock. Appl Environ Microbiol 2024; 90:e0054823. [PMID: 38126750 PMCID: PMC10807460 DOI: 10.1128/aem.00548-23] [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: 04/03/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape maintenance, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Apparently-redundant proteins can be important for enabling an organism to cope with environmental stressors. In this study, we evaluated the consequence of environmental pH on PBP enzymatic activity in Bacillus subtilis. Our data show that a subset of PBPs in B. subtilis change activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are favored for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed in Streptococcus pneumoniae, implying that it may be generalizable across additional bacterial species and further emphasizing the evolutionary benefit of maintaining many, seemingly-redundant periplasmic enzymes.IMPORTANCEMicrobes adapt to ever-changing environments and thrive over a vast range of conditions. While bacterial genomes are relatively small, significant portions encode for "redundant" functions. Apparent redundancy is especially pervasive in bacterial proteins that reside outside of the inner membrane. While conditions within the cytoplasm are carefully controlled, those of the periplasmic space are largely determined by the cell's exterior environment. As a result, proteins within this environmentally exposed region must be capable of functioning under a vast array of conditions, and/or there must be several similar proteins that have evolved to function under a variety of conditions. This study examines the activity of a class of enzymes that is essential in cell wall construction to determine if individual proteins might be adapted for activity under particular growth conditions. Our results indicate that a subset of these proteins are preferred for growth under alkaline conditions, while others are readily dispensable.
Collapse
Affiliation(s)
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
- Departments of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, United States
| |
Collapse
|
4
|
Fihn CA, Lembke HK, Gaulin J, Bouchard P, Villarreal AR, Penningroth MR, Crone KK, Vogt GA, Gilbertsen AJ, Ayotte Y, de Oliveira LC, Serrano-Wu MH, Drouin N, Hung DT, Hunter RC, Carlson EE. Evaluation of Expanded 2-Aminobenzothiazole Library for Inhibition of Pseudomonas aeruginosa Virulence Phenotypes. bioRxiv 2024:2023.05.02.539119. [PMID: 37205454 PMCID: PMC10187220 DOI: 10.1101/2023.05.02.539119] [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: 05/21/2023]
Abstract
Bacterial resistance to antibiotics is a rapidly increasing threat to human health. New strategies to combat resistant organisms are desperately needed. One potential avenue is targeting two-component systems, which are the main bacterial signal transduction pathways used to regulate development, metabolism, virulence, and antibiotic resistance. These systems consist of a homodimeric membrane-bound sensor histidine kinase, and a cognate effector, the response regulator. The high sequence conservation in the catalytic and adenosine triphosphate-binding (CA) domain of histidine kinases and their essential role in bacterial signal transduction could enable broad-spectrum antibacterial activity. Through this signal transduction, histidine kinases regulate multiple virulence mechanisms including toxin production, immune evasion, and antibiotic resistance. Targeting virulence, as opposed to development of bactericidal compounds, could reduce evolutionary pressure for acquired resistance. Additionally, compounds targeting the CA domain have the potential to impair multiple two-component systems that regulate virulence in one or more pathogens. We conducted structure-activity relationship studies of 2-aminobenzothiazole-based inhibitors designed to target the CA domain of histidine kinases. We found these compounds have anti-virulence activities in Pseudomonas aeruginosa, reducing motility phenotypes and toxin production associated with the pathogenic functions of this bacterium.
Collapse
Affiliation(s)
- Conrad A. Fihn
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55454, United States
| | - Jeffrey Gaulin
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Patricia Bouchard
- NMX Research and Solution Inc., 500 Cartier Boulevard W., Suite 6000, Laval, Quebec, Canada, H1Y 2R1
| | - Alex R. Villarreal
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Ave Se Minneapolis, Minnesota 55455, United States
| | - Mitchell R. Penningroth
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Ave Se Minneapolis, Minnesota 55455, United States
| | - Kathryn K. Crone
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Grace A. Vogt
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Ave Se Minneapolis, Minnesota 55455, United States
| | - Adam J. Gilbertsen
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Ave Se Minneapolis, Minnesota 55455, United States
| | - Yann Ayotte
- NMX Research and Solution Inc., 500 Cartier Boulevard W., Suite 6000, Laval, Quebec, Canada, H1Y 2R1
| | | | | | - Nathalie Drouin
- NMX Research and Solution Inc., 500 Cartier Boulevard W., Suite 6000, Laval, Quebec, Canada, H1Y 2R1
| | - Deborah T. Hung
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Ryan C. Hunter
- Department of Microbiology & Immunology, University of Minnesota, 689 23rd Ave Se Minneapolis, Minnesota 55455, United States
| | - Erin E. Carlson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55454, United States
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
5
|
Lembke HK, Carlson EE. Activity-based probes in pathogenic bacteria: Investigating drug targets and molecule specificity. Curr Opin Chem Biol 2023; 76:102359. [PMID: 37406424 PMCID: PMC10526982 DOI: 10.1016/j.cbpa.2023.102359] [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: 04/12/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023]
Abstract
Bacteria comprise complex communities within our bodies and largely have beneficial roles, however a small percentage are pathogenic. While all pathogens are important to public health, immediate action is necessary to combat bacterial strains developing pan- and multi-resistance to antibiotics. As present therapeutics fail to tackle this problem, novel strategies are required to address this threat. Activity-based probes (ABPs) are one method to investigate proteins of interest in pathogens. These probes can serve multiple purposes to better our understanding of bacterial pathogenicity. Herein, we highlight recent studies that used ABPs to identify new drug targets or visualize antibiotic resistance- or bacterial virulence-associated proteins, and introduce strategies to determine the specificity of ABPs within a targeted enzyme class.
Collapse
Affiliation(s)
- Hannah K Lembke
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States; Department of Pharmacology, University of Minnesota, Minneapolis, MN, United States.
| |
Collapse
|
6
|
Lembke HK, Espinasse A, Hanson MG, Grimme CJ, Tan Z, Reineke TM, Carlson EE. Cationic Polymers Enable Internalization of Negatively Charged Chemical Probes into Bacteria. ACS Chem Biol 2023; 18:2063-2072. [PMID: 37671702 PMCID: PMC10947785 DOI: 10.1021/acschembio.3c00351] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
The bacterial cell envelope provides a protective barrier that is challenging for small molecules and biomolecules to cross. Given the anionic nature of both Gram-positive and Gram-negative bacterial cell envelopes, negatively charged molecules are particularly difficult to deliver into these organisms. Many strategies have been employed to penetrate bacteria, ranging from reagents such as cell-penetrating peptides, enzymes, and metal-chelating compounds to physical perturbations. While cationic polymers are known antimicrobial agents, polymers that promote the permeabilization of bacterial cells without causing high levels of toxicity and cell lysis have not yet been described. Here, we investigate four polymers that display a cationic poly(2-(dimethylamino)ethyl methacrylate (D) block for the internalization of an anionic adenosine triphosphate (ATP)-based chemical probe into Escherichia coli and Bacillus subtilis. We evaluated two polymer architectures, linear and micellar, to determine how shape and hydrophobicity affect internalization efficiency. We found that, in addition to these reagents successfully promoting probe internalization, the probe-labeled cells were able to continue to grow and divide. The micellar structures in particular were highly effective for the delivery of the negatively charged chemical probe. Finally, we demonstrated that these cationic polymers could act as general permeabilization reagents, promoting the entry of other molecules, such as antibiotics.
Collapse
Affiliation(s)
- Hannah K Lembke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adeline Espinasse
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mckenna G Hanson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christian J Grimme
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Zhe Tan
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
7
|
Espinasse A, Goswami M, Yang J, Vorasin O, Ji Y, Carlson EE. Targeting multidrug resistant Staphylococcus infections with bacterial histidine kinase inhibitors. Chem Sci 2023; 14:5028-5037. [PMID: 37206395 PMCID: PMC10189854 DOI: 10.1039/d2sc05369a] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/10/2023] [Indexed: 05/21/2023] Open
Abstract
The emergence of drug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), which are not susceptible to current antibiotics has necessitated the development of novel approaches and targets to tackle this growing challenge. Bacterial two-component systems (TCSs) play a central role in the adaptative response of bacteria to their ever-changing environment. They are linked to antibiotic resistance and bacterial virulence making the proteins of the TCSs, histidine kinases and response regulators, attractive for the development of novel antibacterial drugs. Here, we developed a suite of maleimide-based compounds that we evaluated against a model histidine kinase, HK853, in vitro and in silico. The most potent leads were then assessed for their ability to decrease the pathogenicity and virulence of MRSA, resulting in the identification of a molecule that decreased the lesion size caused by a methicillin-resistant S. aureus skin infection by 65% in a murine model.
Collapse
Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota 225 Pleasant St. SE Minneapolis 55454 MN USA
| | - Manibarsha Goswami
- Department of Chemistry, University of Minnesota 225 Pleasant St. SE Minneapolis 55454 MN USA
| | - Junshu Yang
- Department of Veterinary and Biomedical Sciences, University of Minnesota 1971 Commonwealth Ave Falcon Heights 55108 MN USA
| | - Onanong Vorasin
- Department of Chemistry, University of Minnesota 225 Pleasant St. SE Minneapolis 55454 MN USA
- Department of Chemistry, Faculty of Science, Mahidol University Rama 6 Road Bangkok 10400 Thailand
| | - Yinduo Ji
- Department of Veterinary and Biomedical Sciences, University of Minnesota 1971 Commonwealth Ave Falcon Heights 55108 MN USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota 225 Pleasant St. SE Minneapolis 55454 MN USA
- Department of Medicinal Chemistry, University of Minnesota 208 Harvard Street SE Minneapolis 55454 Minnesota USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota 321 Church St SE Minneapolis 55454 Minnesota USA
- Department of Pharmacology, University of Minnesota 321 Church St SE Minneapolis 55454 Minnesota USA
| |
Collapse
|
8
|
Mitchell SL, Kearns DB, Carlson EE. Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock. bioRxiv 2023:2023.03.20.533529. [PMID: 36993441 PMCID: PMC10055284 DOI: 10.1101/2023.03.20.533529] [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] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Seemingly redundant proteins can be important for enabling an organism to cope with environmental stressors. We sought to evaluate the consequence of environmental pH on PBP enzymatic activity in Bacillus subtilis. Our data show that a subset of B. subtilis PBPs change activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are preferred for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed in Streptococcus pneumoniae, implying that it may be generalizable across additional bacterial species and further emphasizing the evolutionary benefit of maintaining many, seemingly redundant periplasmic enzymes.
Collapse
Affiliation(s)
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Departments of Medicinal Chemistry, Biochemistry, Molecular Biology and Biophysics, and Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
| |
Collapse
|
9
|
Marshall AP, Carlson EE. Metabolomics Reveals a "Trimeric" γ-Actinorhodin from Streptomyces coelicolor M145. Chembiochem 2023; 24:e202200757. [PMID: 36729633 DOI: 10.1002/cbic.202200757] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/03/2023]
Abstract
Streptomyces coelicolor is a prolific producer of natural products and serves as a model organism for their study. It produces several pigmented antibiotics, the best-studied of which are the actinorhodins. We used a combination of liquid chromatography-mass spectrometry (LC-MS) and computational tools used for annotating the detected species (e. g., spectral matching, in-silico predictors, molecular networking) to identify putative new actinorhodin analogs. These studies led to the discovery of the first trimeric benzoisochromanequinone, θ-actinorhodin (1). Further metabolomics analysis revealed that the relative amounts of shunt products produced were similar between the two growth conditions explored. This suggests that, while substantially different products were being produced, the biosynthetic gene clusters were similarly active. Overall, this work describes the discovery of the first trimeric benzoisochromanequinone and explores the biosynthetic processes that might lead to its production by metabolomics analysis of relevant intermediates.
Collapse
Affiliation(s)
- Andrew P Marshall
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota, 55455, USA.,Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota, 55454, USA.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church St SE, Minneapolis, Minnesota, 55454, USA.,Department of Pharmacology, University of Minnesota, 321 Church St SE, Minneapolis, Minnesota, 55454, USA
| |
Collapse
|
10
|
Flanders PL, Contreras-Martel C, Brown NW, Shirley JD, Martins A, Nauta KN, Dessen A, Carlson EE, Ambrose EA. Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with β-Lactones. ACS Chem Biol 2022; 17:3110-3120. [PMID: 36173746 PMCID: PMC10057605 DOI: 10.1021/acschembio.2c00503] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
β-Lactam antibiotics comprise one of the most widely used therapeutic classes to combat bacterial infections. This general scaffold has long been known to inhibit bacterial cell wall biosynthesis by inactivating penicillin-binding proteins (PBPs); however, bacterial resistance to β-lactams is now widespread, and new strategies are urgently needed to target PBPs and other proteins involved in bacterial cell wall formation. A key requirement in the identification of strategies to overcome resistance is a deeper understanding of the roles of the PBPs and their associated proteins during cell growth and division, such as can be obtained with the use of selective chemical probes. Probe development has typically depended upon known PBP inhibitors, which have historically been thought to require a negatively charged moiety that mimics the C-terminus of the PBP natural peptidoglycan substrate, d-Ala-d-Ala. However, we have identified a new class of β-lactone-containing molecules that interact with PBPs, often in an isoform-specific manner, and do not incorporate this C-terminal mimetic. Here, we report a series of structural biology experiments and molecular dynamics simulations that we utilized to evaluate specific binding modes of this novel PBP inhibitor class. In this work, we obtained <2 Å resolution X-ray structures of four β-lactone probes bound to PBP1b from Streptococcus pneumoniae. Despite their diverging recognition modes beyond the site of covalent modification, these four probes all efficiently labeled PBP1b, as well as other PBPs from S. pneumoniae. From these structures, we analyzed protein-ligand interactions and characterized the β-lactone-bound active sites using in silico mutagenesis and molecular dynamics. Our approach has clarified the dynamic interaction profile in this series of ligands, expanding the understanding of PBP inhibitor binding.
Collapse
Affiliation(s)
- Parker L Flanders
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
| | - Carlos Contreras-Martel
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
| | - Nathaniel W Brown
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
| | - Alexandre Martins
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
| | - Kelsie N Nauta
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Andréa Dessen
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France.,Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, São Paulo, Brazil
| | - Erin E Carlson
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States.,Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States.,Department of Pharmacology, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States
| | - Elizabeth A Ambrose
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States.,Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
11
|
Olson NM, Johnson JA, Peterson KE, Henisch SC, Marshall AP, Smanski MJ, Carlson EE, Pomerantz WC. Development of a single culture E. coli expression system for the enzymatic synthesis of fluorinated tyrosine and its incorporation into proteins. J Fluor Chem 2022; 261-262. [PMID: 37197608 PMCID: PMC10187777 DOI: 10.1016/j.jfluchem.2022.110014] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Current experiments that rely on biosynthetic metabolic protein labeling with 19F often require fluorinated amino acids, which in the case of 2- and 3-fluorotyrosine can be expensive. However, using these amino acids has provided valuable insight into protein dynamics, structure, and function. Here, we develop a new in-cell method for fluorinated tyrosine generation from readily available substituted phenols and subsequent metabolic labeling of proteins in a single bacterial expression culture. This approach uses a dual-gene plasmid encoding for a model protein BRD4(D1) and a tyrosine phenol lyase from Citrobacter freundii, which catalyzes the formation of tyrosine from phenol, pyruvate, and ammonium. Our system demonstrated both enzymatic fluorotyrosine production and expression of 19F-labeled proteins as analyzed by 19F NMR and LC-MS methods. Further optimization of our system should provide a cost-effective alternative to a variety of traditional protein-labeling strategies.
Collapse
|
12
|
Fasching PA, Liu D, Scully S, Ingle JN, Lyra PC, Rack B, Hein A, Ekici AB, Reis A, Schneeweiss A, Tesch H, Fehm TN, Heinrich G, Beckmann MW, Ruebner M, Huebner H, Lambrechts D, Madden E, Shen J, Romm J, Doheny K, Jenkins GD, Carlson EE, Li L, Fridley BL, Cunningham JM, Janni W, Monteiro ANA, Schaid DJ, Häberle L, Weinshilboum RM, Wang L. Identification of Two Genetic Loci Associated with Leukopenia after Chemotherapy in Patients with Breast Cancer. Clin Cancer Res 2022; 28:3342-3355. [PMID: 35653140 PMCID: PMC9357161 DOI: 10.1158/1078-0432.ccr-20-4774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/09/2020] [Revised: 01/20/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023]
Abstract
PURPOSE To identify molecular predictors of grade 3/4 neutropenic or leukopenic events (NLE) after chemotherapy using a genome-wide association study (GWAS). EXPERIMENTAL DESIGN A GWAS was performed on patients in the phase III chemotherapy study SUCCESS-A (n = 3,322). Genotyping was done using the Illumina HumanOmniExpress-12v1 array. Findings were functionally validated with cell culture models and the genotypes and gene expression of possible causative genes were correlated with clinical treatment response and prognostic outcomes. RESULTS One locus on chromosome 16 (rs4784750; NLRC5; P = 1.56E-8) and another locus on chromosome 13 (rs16972207; TNFSF13B; P = 3.42E-8) were identified at a genome-wide significance level. Functional validation revealed that expression of these two genes is altered by genotype-dependent and chemotherapy-dependent activity of two transcription factors. Genotypes also showed an association with disease-free survival in patients with an NLE. CONCLUSIONS Two loci in NLRC5 and TNFSF13B are associated with NLEs. The involvement of the MHC I regulator NLRC5 implies the possible involvement of immuno-oncological pathways.
Collapse
Affiliation(s)
- Peter A Fasching
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Steve Scully
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - James N Ingle
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Paulo C Lyra
- Biotechnology/RENORBIO Program, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Brigitte Rack
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Andre Reis
- Institute of Human Genetics, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Division of Gynecologic Oncology, Heidelberg University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Hans Tesch
- Onkologie Bethanien, Frankfurt am Main, Germany
| | - Tanja N Fehm
- Department of Gynecology and Obstetrics, Düsseldorf University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Georg Heinrich
- Schwerpunktpraxis für Gynäkologische Onkologie, Fürstenwalde, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Matthias Ruebner
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Hanna Huebner
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB and Laboratory for Translational Genetics, KU Leuven, Leuven, Belgium
| | - Ebony Madden
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, Maryland
| | - Jess Shen
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jane Romm
- McKusick-Nathans Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Kim Doheny
- McKusick-Nathans Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Gregory D Jenkins
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Erin E Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Liang Li
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
- Department of Oncology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Tiantan Xili, Beijing, China
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Lothar Häberle
- Department of Gynecology and Obstetrics, University Breast Center for Franconia, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen EMN, Erlangen, Germany
- Department of Gynecology and Obstetrics, Unit of Biostatistics, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
13
|
Abstract
Penicillin-binding proteins (PBPs) make up an essential class of bacterial enzymes that carry out the final steps of peptidoglycan synthesis and regulate the recycling of this polymeric structure. PBPs are an excellent drug target and have been the most clinically relevant antibacterial target since the 1940s with the introduction of β-lactams. Despite this, a large gap in knowledge remains regarding the individual function and regulation of each PBP homologue in most bacteria. This can be attributed to a lack of chemical tools and methods that enable the study of individual PBPs in an activity-dependent manner and in their native environment. The development of such methods in Gram-negative bacteria has been particularly challenging due to the presence of an outer membrane and numerous resistance mechanisms. To address this, we have developed an optimized live-cell assay for screening inhibitors of the PBPs in Escherichia coli MG1655. We utilized EDTA to permeabilize Gram-negative cells, enabling increased penetration of our readout probe, Bocillin-FL, and subsequent analysis of PBP-inhibition profiles. To identify scaffolds for future development of PBP-selective activity-based probes, we screened ten β-lactams, one diazabicyclooctane, and one monobactam for their PBP-selectivity profiles in E. coli MG1655. These results demonstrate the utility of our assay for the screening of inhibitors in live, non-hypersusceptible Gram-negative organisms.
Collapse
Affiliation(s)
- Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
| | - Kelsie M Nauta
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Erin E Carlson
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States.,Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States.,Department of Pharmacology, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States
| |
Collapse
|
14
|
Lembke HK, Carlson EE. Activity-based ATP analog probes for bacterial histidine kinases. Methods Enzymol 2022; 664:59-84. [PMID: 35331379 DOI: 10.1016/bs.mie.2022.01.003] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Histidine kinases (HKs) are sensor proteins found ubiquitously in prokaryotes. They are the first protein in two-component systems (TCSs), signaling pathways that respond to a myriad of environmental stimuli. TCSs are typically comprised of a HK and its cognate response regulator (RR) which often acts as a transcription factor. RRs will bind DNA and ultimately lead to a cellular response. These cellular outputs vary widely, but HKs are particularly interesting as they are tied to antibiotic resistance and virulence pathways in pathogenic bacteria, making them promising drug targets. We anticipate that HK inhibitors could serve as either standalone antibiotics or antivirulence therapies. Additionally, while the cellular response mediated by the HKs is often well-characterized, very little is known about which stimuli trigger the sensor kinase to begin the phosphorylation cascade. Studying HK activity and enrichment of active HKs through activity-based protein profiling will enable these stimuli to be elucidated, filling this fundamental gap in knowledge. Here, we describe methods to evaluate the potency of putative HK inhibitors in addition to methods to calculate kinetic parameters of various activity-based probes designed for the HKs.
Collapse
Affiliation(s)
- Hannah K Lembke
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States; Department of Pharmacology, University of Minnesota, Minneapolis, MN, United States.
| |
Collapse
|
15
|
Sharan D, Carlson EE. Expanded profiling of β-lactam selectivity for penicillin-binding proteins in Streptococcus pneumoniae D39. Biol Chem 2022; 403:433-443. [PMID: 35218689 DOI: 10.1515/hsz-2021-0386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 10/06/2021] [Accepted: 02/10/2022] [Indexed: 12/17/2022]
Abstract
Penicillin-binding proteins (PBPs) are integral to bacterial cell division as they mediate the final steps of cell wall maturation. Selective fluorescent probes are useful for understanding the role of individual PBPs, including their localization and activity during growth and division of bacteria. For the development of new selective probes for PBP imaging, several β-lactam antibiotics were screened, as they are known to covalently bind PBP in vivo. The PBP inhibition profiles of 16 commercially available β-lactam antibiotics were evaluated in an unencapsulated derivative of the D39 strain of Streptococcus pneumoniae, IU1945. These β-lactams have not previously been characterized for their PBP inhibition profiles in S. pneumoniae and these data augment those obtained from a library of 20 compounds that we previously reported. We investigated seven penicillins, three carbapenems, and six cephalosporins. Most of these β-lactams were found to be co-selective for PBP2x and PBP3, as was noted in our previous studies. Six out of 16 antibiotics were selective for PBP3 and one molecule was co-selective for PBP1a and PBP3. Overall, this work expands the chemical space available for development of future β-lactam-based probes for specific pneumococcal PBP labeling and these methods can be used for the development of probes for PBP labelling in other bacterial species.
Collapse
Affiliation(s)
- Deepti Sharan
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA.,Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, MN 55454, USA.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, USA.,Department of Pharmacology, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, USA
| |
Collapse
|
16
|
Murtha AN, Kazi MI, Schargel RD, Cross T, Fihn C, Cattoir V, Carlson EE, Boll JM, Dörr T. High-level carbapenem tolerance requires antibiotic-induced outer membrane modifications. PLoS Pathog 2022; 18:e1010307. [PMID: 35130322 PMCID: PMC8853513 DOI: 10.1371/journal.ppat.1010307] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 11/01/2021] [Revised: 02/17/2022] [Accepted: 01/26/2022] [Indexed: 12/22/2022] Open
Abstract
Antibiotic tolerance is an understudied potential contributor to antibiotic treatment failure and the emergence of multidrug-resistant bacteria. The molecular mechanisms governing tolerance remain poorly understood. A prominent type of β-lactam tolerance relies on the formation of cell wall-deficient spheroplasts, which maintain structural integrity via their outer membrane (OM), an asymmetric lipid bilayer consisting of phospholipids on the inner leaflet and a lipid-linked polysaccharide (lipopolysaccharide, LPS) enriched in the outer monolayer on the cell surface. How a membrane structure like LPS, with its reliance on mere electrostatic interactions to maintain stability, is capable of countering internal turgor pressure is unknown. Here, we have uncovered a novel role for the PhoPQ two-component system in tolerance to the β-lactam antibiotic meropenem in Enterobacterales. We found that PhoPQ is induced by meropenem treatment and promotes an increase in 4-amino-4-deoxy-L-aminoarabinose [L-Ara4N] modification of lipid A, the membrane anchor of LPS. L-Ara4N modifications likely enhance structural integrity, and consequently tolerance to meropenem, in several Enterobacterales species. Importantly, mutational inactivation of the negative PhoPQ regulator mgrB (commonly selected for during clinical therapy with the last-resort antibiotic colistin, an antimicrobial peptide [AMP]) results in dramatically enhanced tolerance, suggesting that AMPs can collaterally select for meropenem tolerance via stable overactivation of PhoPQ. Lastly, we identify histidine kinase inhibitors (including an FDA-approved drug) that inhibit PhoPQ-dependent LPS modifications and consequently potentiate meropenem to enhance lysis of tolerant cells. In summary, our results suggest that PhoPQ-mediated LPS modifications play a significant role in stabilizing the OM, promoting survival when the primary integrity maintenance structure, the cell wall, is removed. Treating an infection with an antibiotic often fails, resulting in a tremendous public health burden. One understudied likely reason for treatment failure is the development of “antibiotic tolerance”, the ability of bacteria to survive normally lethal exposure to an antibiotic. Here, we describe a molecular mechanism promoting tolerance. A bacterial stress sensor (PhoPQ) is activated in response to antibiotic (meropenem) treatment and consequently strengthens a bacterial protective “shell” to enhance survival. We also identify inhibitors of this mechanism, opening the door to developing compounds that help antibiotics work better against tolerant bacteria.
Collapse
Affiliation(s)
- Andrew N. Murtha
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Misha I. Kazi
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
| | - Richard D. Schargel
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
| | - Trevor Cross
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Conrad Fihn
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Vincent Cattoir
- Department of Clinical Microbiology and National Reference Center for Antimicrobial Resistance (Lab Enterococci), Rennes University Hospital, Rennes, France; Inserm Unit U1230, University of Rennes 1, Rennes, France
| | - Erin E. Carlson
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Molecular Pharmacology and Therapeutics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Joseph M. Boll
- Department of Biology, University of Texas Arlington, Arlington, Texas, United States of America
- * E-mail: (JMB); (TD)
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, United States of America
- * E-mail: (JMB); (TD)
| |
Collapse
|
17
|
|
18
|
|
19
|
Cairns J, Kalari KR, Ingle JN, Shepherd LE, Ellis MJ, Goss PE, Barman P, Carlson EE, Goodnature B, Goetz MP, Weinshilboum RM, Gao H, Wang L. Interaction Between SNP Genotype and Efficacy of Anastrozole and Exemestane in Early-Stage Breast Cancer. Clin Pharmacol Ther 2021; 110:1038-1049. [PMID: 34048027 PMCID: PMC8449801 DOI: 10.1002/cpt.2311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/24/2021] [Accepted: 05/08/2021] [Indexed: 12/24/2022]
Abstract
Aromatase inhibitors (AIs) are the treatment of choice for hormone receptor-positive early breast cancer in postmenopausal women. None of the third-generation AIs are superior to the others in terms of efficacy. We attempted to identify genetic factors that could differentiate between the effectiveness of adjuvant anastrozole and exemestane by examining single-nucleotide polymorphism (SNP)-treatment interaction in 4,465 patients. A group of SNPs were found to be differentially associated between anastrozole and exemestane regarding outcomes. However, they showed no association with outcome in the combined analysis. We followed up common SNPs near LY75 and GPR160 that could differentiate anastrozole from exemestane efficacy. LY75 and GPR160 participate in epithelial-to-mesenchymal transition and growth pathways, in both cases with SNP-dependent variation in regulation. Collectively, these studies identified SNPs that differentiate the efficacy of anastrozole and exemestane and they suggest additional genetic biomarkers for possible use in selecting an AI for a given patient.
Collapse
Affiliation(s)
- Junmei Cairns
- Division of Clinical PharmacologyDepartment of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Krishna R. Kalari
- Division of Biomedical Statistics and InformaticsDepartment of Health Sciences ResearchMayo ClinicRochesterMinnesotaUSA
| | - James N. Ingle
- Division of Medical OncologyDepartment of OncologyMayo ClinicRochesterMinnesotaUSA
| | | | - Matthew J. Ellis
- Department of MedicineBaylor University College of MedicineHoustonTexasUSA
| | - Paul E. Goss
- Massachusetts General Hospital Cancer CenterHarvard UniversityBostonMassachusettsUSA
| | - Poulami Barman
- Division of Biomedical Statistics and InformaticsDepartment of Health Sciences ResearchMayo ClinicRochesterMinnesotaUSA
| | - Erin E. Carlson
- Division of Biomedical Statistics and InformaticsDepartment of Health Sciences ResearchMayo ClinicRochesterMinnesotaUSA
| | - Barbara Goodnature
- Patient AdvocateMayo Clinic Breast Cancer Specialized Program of Research ExcellenceRochesterMinnesotaUSA
| | - Matthew P. Goetz
- Division of Medical OncologyDepartment of OncologyMayo ClinicRochesterMinnesotaUSA
| | - Richard M. Weinshilboum
- Division of Clinical PharmacologyDepartment of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Huanyao Gao
- Division of Clinical PharmacologyDepartment of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Liewei Wang
- Division of Clinical PharmacologyDepartment of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| |
Collapse
|
20
|
Fihn CA, Carlson EE. Targeting a highly conserved domain in bacterial histidine kinases to generate inhibitors with broad spectrum activity. Curr Opin Microbiol 2021; 61:107-114. [PMID: 33932730 DOI: 10.1016/j.mib.2021.03.007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/30/2022]
Abstract
With the rise in antimicrobial resistance and the dearth of effective strategies to combat this threat, the development of novel therapies is of utmost importance. Targeting of bacterial signaling through their the two-component systems (TCSs) may be a viable strategy. TCSs are comprised of a sensory histidine kinase (HK), of which a bacterium can have up to 160 distinct proteins, and a cognate response regulator (RR). The TCSs are generally non-essential for life, but control many virulence and antibiotic-resistance mechanisms. This, along with their absence in animals makes the TCSs an attractive target for antimicrobial therapy, whether as a stand-alone treatments or adjuvants for existing therapies. This review focuses on progress in the development of inhibitors that target the HK ATP-binding domain. Because this domain is highly conserved, it may be feasible to disrupt multiple TCSs within a single organism to increase effectiveness and reduce pressure for the evolution of resistance.
Collapse
Affiliation(s)
- Conrad A Fihn
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55454, United States
| | - Erin E Carlson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55454, United States; Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, United States; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, United States; Department of Pharmacology, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, United States.
| |
Collapse
|
21
|
Brown NW, Shirley JD, Marshall AP, Carlson EE. Comparison of Bioorthogonal β-Lactone Activity-Based Probes for Selective Labeling of Penicillin-Binding Proteins. Chembiochem 2021; 22:193-202. [PMID: 32964667 PMCID: PMC7790944 DOI: 10.1002/cbic.202000556] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/06/2020] [Revised: 09/21/2020] [Indexed: 01/20/2023]
Abstract
Penicillin-binding proteins (PBPs) are a family of bacterial enzymes that are key components of cell-wall biosynthesis and the target of β-lactam antibiotics. Most microbial pathogens contain multiple structurally homologous PBP isoforms, making it difficult to target individual PBPs. To study the roles and regulation of specific PBP isoforms, a panel of bioorthogonal β-lactone probes was synthesized and compared. Fluorescent labeling confirmed selectivity, and PBPs were selectively enriched from Streptococcus pneumoniae lysates. Comparisons between fluorescent labeling of probes revealed that the accessibility of bioorthogonal reporter molecules to the bound probe in the native protein environment exerts a more significant effect on labeling intensity than the bioorthogonal reaction used, observations that are likely applicable beyond this class of probes or proteins. Selective, bioorthogonal activity-based probes for PBPs will facilitate the activity-based determination of the roles and regulation of specific PBP isoforms, a key gap in knowledge that has yet to be filled.
Collapse
Affiliation(s)
- Nathaniel W Brown
- Department of Chemistry, University of Minnesota-Twin Cities 139 Smith Hall, Pleasant Street SE, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Andrew P Marshall
- Department of Chemistry, University of Minnesota-Twin Cities 139 Smith Hall, Pleasant Street SE, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities 139 Smith Hall, Pleasant Street SE, Minneapolis, MN, 55455, USA
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, 321 Church Street SE, Minneapolis, MN, 55455, USA
| |
Collapse
|
22
|
Ingle JN, Kalari KR, Barman P, Shepherd LE, Ellis MJ, Goss PE, Buzdar AU, Robson ME, Cairns J, Carlson EE, Casey AE, Hoskin TL, Goodnature BA, Haddad TC, Goetz MP, Weinshilboum RM, Wang L. Single-nucleotide polymorphism biomarkers of adjuvant anastrozole-induced estrogen suppression in early breast cancer. Pharmacogenet Genomics 2021; 31:1-9. [PMID: 32649577 PMCID: PMC7655717 DOI: 10.1097/fpc.0000000000000415] [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: 02/01/2023]
Abstract
OBJECTIVES Based on our previous findings that postmenopausal women with estrone (E1) and estradiol (E2) concentrations at or above 1.3 pg/ml and 0.5 pg/ml, respectively, after 6 months of adjuvant anastrozole therapy had a three-fold risk of recurrence, we aimed to identify a single-nucleotide polymorphism (SNP)-based model that would predict elevated E1 and E2 and then validate it in an independent dataset. PATIENTS AND METHODS The test set consisted of 322 women from the M3 study and the validation set consisted of 152 patients from MA.27. All patients were treated with adjuvant anastrozole, had on-anastrozole E1 and E2 concentrations and genome-wide genotyping. RESULTS SNPs were identified from the M3 genome-wide association study. The best model to predict the E1-E2 phenotype with high balanced accuracy was a support vector machine model using clinical factors plus 46 SNPs. We did not have an independent cohort that is similar to the M3 study with clinical, E1-E2 phenotypes and genotype data to test our model. Hence, we chose a nested matched case-control cohort (MA.27 study) for testing. Our E1-E2 model was not validated but we found the MA.27 validation cohort was both clinically and genomically different. CONCLUSIONS We identified a SNP-based model that had excellent performance characteristics for predicting the phenotype of elevated E1 and E2 in women treated with anastrozole. This model was not validated in an independent dataset but that dataset was clinically and genomically substantially different. The model will need validation in a prospective study.
Collapse
Affiliation(s)
- James N. Ingle
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN
| | - Krishna R. Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Poulami Barman
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | - Paul E. Goss
- Massachusetts General Hospital Cancer Center, Harvard University, Boston, MA
| | - Aman U. Buzdar
- Department of Breast Oncology, M.D. Anderson Cancer Center, Houston, TX
| | - Mark E. Robson
- Breast Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Junmei Cairns
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN
| | - Erin E. Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Abraham Eyman Casey
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Tanya L. Hoskin
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Barbara A. Goodnature
- Patient advocate, Mayo Clinic Breast Cancer Specialized Program of Research Excellence, Rochester, MN
| | - Tufia C. Haddad
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN
| | - Matthew P. Goetz
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN
| | - Richard M. Weinshilboum
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Liewei Wang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| |
Collapse
|
23
|
Perez AJ, Boersma MJ, Bruce KE, Lamanna MM, Shaw SL, Tsui HCT, Taguchi A, Carlson EE, VanNieuwenhze MS, Winkler ME. Organization of peptidoglycan synthesis in nodes and separate rings at different stages of cell division of Streptococcus pneumoniae. Mol Microbiol 2020; 115:1152-1169. [PMID: 33269494 DOI: 10.1111/mmi.14659] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/15/2022]
Abstract
Bacterial peptidoglycan (PG) synthesis requires strict spatiotemporal organization to reproduce specific cell shapes. In ovoid-shaped Streptococcus pneumoniae (Spn), septal and peripheral (elongation) PG synthesis occur simultaneously at midcell. To uncover the organization of proteins and activities that carry out these two modes of PG synthesis, we examined Spn cells vertically oriented onto their poles to image the division plane at the high lateral resolution of 3D-SIM (structured-illumination microscopy). Labeling with fluorescent D-amino acids (FDAA) showed that areas of new transpeptidase (TP) activity catalyzed by penicillin-binding proteins (PBPs) separate into a pair of concentric rings early in division, representing peripheral PG (pPG) synthesis (outer ring) and the leading-edge (inner ring) of septal PG (sPG) synthesis. Fluorescently tagged PBP2x or FtsZ locate primarily to the inner FDAA-marked ring, whereas PBP2b and FtsX remain in the outer ring, suggesting roles in sPG or pPG synthesis, respectively. Pulses of FDAA labeling revealed an arrangement of separate regularly spaced "nodes" of TP activity around the division site of predivisional cells. Tagged PBP2x, PBP2b, and FtsX proteins also exhibited nodal patterns with spacing comparable to that of FDAA labeling. Together, these results reveal new aspects of spatially ordered PG synthesis in ovococcal bacteria during cell division.
Collapse
Affiliation(s)
- Amilcar J Perez
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Michael J Boersma
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Kevin E Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Melissa M Lamanna
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Sidney L Shaw
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Ho-Ching T Tsui
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Atsushi Taguchi
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | | | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| |
Collapse
|
24
|
Cairns J, Ly RC, Niu N, Kalari KR, Carlson EE, Wang L. CDC25B partners with PP2A to induce AMPK activation and tumor suppression in triple negative breast cancer. NAR Cancer 2020; 2:zcaa039. [PMID: 33385163 PMCID: PMC7751685 DOI: 10.1093/narcan/zcaa039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 07/16/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 12/28/2022] Open
Abstract
Cell division cycle 25 (CDC25) dual specificity phosphatases positively regulate the cell cycle by activating cyclin-dependent kinase/cyclin complexes. Here, we demonstrate that in addition to its role in cell cycle regulation, CDC25B functions as a regulator of protein phosphatase 2A (PP2A), a major cellular Ser/Thr phosphatase, through its direct interaction with PP2A catalytic subunit. Importantly, CDC25B alters the regulation of AMP-activated protein kinase signaling (AMPK) by PP2A, increasing AMPK activity by inhibiting PP2A to dephosphorylate AMPK. CDC25B depletion leads to metformin resistance by inhibiting metformin-induced AMPK activation. Furthermore, dual inhibition of CDC25B and PP2A further inhibits growth of 3D organoids isolated from patient derived xenograft model of breast cancer compared to CDC25B inhibition alone. Our study identifies CDC25B as a regulator of PP2A, and uncovers a mechanism of controlling the activity of a key energy metabolism marker, AMPK.
Collapse
Affiliation(s)
- Junmei Cairns
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Reynold C Ly
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nifang Niu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna R Kalari
- Division of Biostatistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Erin E Carlson
- Division of Biostatistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- To whom correspondence should be addressed. Tel: +1 507 284 5264; Fax: +1 507 284 4455;
| |
Collapse
|
25
|
Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
Collapse
Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
| |
Collapse
|
26
|
Thielen MK, Vaneerd CK, Goswami M, Carlson EE, May JF. 2-Aminobenzothiazoles Inhibit Virulence Gene Expression and Block Polymyxin Resistance in Salmonella enterica. Chembiochem 2020; 21:3500-3503. [PMID: 32750193 DOI: 10.1002/cbic.202000422] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Indexed: 01/01/2023]
Abstract
One promising strategy to combat antibiotic-resistant bacteria is to develop compounds that block bacterial defenses against antibacterial conditions produced by the innate immune system. Salmonella enterica, which causes food-borne gastroenteritis and typhoid fever, requires histidine kinases (HKs) to resist innate immune defenses such as cationic antimicrobial peptides (CAMPs). Herein, we report that 2-aminobenzothiazoles block histidine kinase-dependent phenotypes in Salmonella enterica serotype Typhimurium. We found that 2-aminobenzothiazoles inhibited growth under low Mg2+ , a stressful condition that requires histidine kinase-mediated responses, and decreased expression of the virulence genes pagC and pagK. Furthermore, we discovered that 2-aminobenzothiazoles weaken Salmonella's resistance to polymyxin B and polymyxin E, which are last-line antibiotics and models for host defense CAMPs. These findings raise the possibilities that 2-aminobenzothiazoles can block HK-mediated bacterial defenses and can be used in combination with polymyxins to treat infections caused by Salmonella.
Collapse
Affiliation(s)
- Michaela K Thielen
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State St, La Crosse, WI 54601, USA
| | - Cody K Vaneerd
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State St, La Crosse, WI 54601, USA
| | - Manibarsha Goswami
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA
| | - John F May
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State St, La Crosse, WI 54601, USA
| |
Collapse
|
27
|
Cairns J, Ingle JN, Dudenkov TM, Kalari KR, Carlson EE, Na J, Buzdar AU, Robson ME, Ellis MJ, Goss PE, Shepherd LE, Goodnature B, Goetz MP, Weinshilboum RM, Li H, Bari MG, Wang L. Pharmacogenomics of aromatase inhibitors in postmenopausal breast cancer and additional mechanisms of anastrozole action. JCI Insight 2020; 5:137571. [PMID: 32701512 PMCID: PMC7455128 DOI: 10.1172/jci.insight.137571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 02/25/2020] [Accepted: 07/15/2020] [Indexed: 01/09/2023] Open
Abstract
Aromatase inhibitors (AIs) reduce breast cancer recurrence and prolong survival, but up to 30% of patients exhibit recurrence. Using a genome-wide association study of patients entered on MA.27, a phase III randomized trial of anastrozole versus exemestane, we identified a single nucleotide polymorphism (SNP) in CUB And Sushi multiple domains 1 (CSMD1) associated with breast cancer–free interval, with the variant allele associated with fewer distant recurrences. Mechanistically, CSMD1 regulates CYP19 expression in an SNP- and drug-dependent fashion, and this regulation is different among 3 AIs: anastrozole, exemestane, and letrozole. Overexpression of CSMD1 sensitized AI-resistant cells to anastrozole but not to the other 2 AIs. The SNP in CSMD1 that was associated with increased CSMD1 and CYP19 expression levels increased anastrozole sensitivity, but not letrozole or exemestane sensitivity. Anastrozole degrades estrogen receptor α (ERα), especially in the presence of estradiol (E2). ER+ breast cancer organoids and AI- or fulvestrant-resistant breast cancer cells were more sensitive to anastrozole plus E2 than to AI alone. Our findings suggest that the CSMD1 SNP might help to predict AI response, and anastrozole plus E2 serves as a potential new therapeutic strategy for patients with AI- or fulvestrant-resistant breast cancers. A germline variation within the CSMD1 gene predicts aromatase inhibitor response in breast cancer.
Collapse
Affiliation(s)
- Junmei Cairns
- Department of Molecular Pharmacology and Experimental Therapeutics
| | | | - Tanda M Dudenkov
- Department of Molecular Pharmacology and Experimental Therapeutics
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Erin E Carlson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Jie Na
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Aman U Buzdar
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Paul E Goss
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Barbara Goodnature
- Patient advocate, Mayo Clinic Breast Cancer Specialized Program of Research Excellence, Rochester, Minnesota, USA
| | | | | | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics
| | | | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics
| |
Collapse
|
28
|
Cairns J, Ingle JN, Kalari KR, Shepherd LE, Ellis MJ, Goss PE, Barman P, Carlson EE, Goetz MP, Weinshilboum RM, Wang L. Abstract LB-103: The interaction between SNP genotype and aromatase inhibitor treatment response in early breast cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-lb-103] [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
Purpose: To determine genetic variants that could differentiate aromatase inhibitors (AIs) efficacy in early stage breast cancer. Experimental Design: We performed a stratified cox-proportional hazards analysis utilizing stratification factors and other covariates examining Breast Cancer Free Interval (BCFI) SNP-treatment interaction in Caucasian patients entered on the MA.27 trial. This analysis involved 4465 patients (2226 on anastrozole and 2239 on exemestane arm) including 245 (121 on anastrozole and 124 events on exemestane arm) with a breast event. Preclinical laboratory studies included luciferase activity, chromatin immunoprecipitation (ChIP) assay, and cell migration assays. Results: We identified 887 SNPs with a p-value <1E-4 that could differentiate anastrozole from exemestane efficacy. We next used GTEx databases to determine whether these SNPs might be cis-eQTLs with nearby genes, and found that 95 SNPs were eQTL with 14 genes. Functional validation of SNP effect in these 14 genes on response to anastrozole and exemestane revealed that 3 SNPs showed genotype-dependent differences between anastrozole and exemestane. Two of the three SNPs, rs1877193 and rs6735923 located upstream of LY75 gene, were associated with higher LY75 gene expression. Our drug-SNP interaction GWAS showed that both SNPs were associated with better BCFI for exemestane compared to anastrozole (HR= 0.447, 0.458). The SNP rs62293499 located downstream of the GPR160 gene was also associated with better BCFI for exemestane compared to anastrozole (HR=0.433). Interestingly, all 3 SNPs were associated with worse outcome (shorter BCFI) in anastrozole treated patients (HR=1.39~1.58), but with longer BCFI in the exemestane treated patients (HR=0.58~0.71) based on our GWAS results in MA.27 trial. However, all 3 SNPs showed no association with BCFI if the two treatment arms, anastrozole and exemestane, were combined (HR=0.92~1.08). Consistently, cells with Ly75 or GPR160 SNP variant genotypes were more sensitive to exemestane compared to anastrozole. Mechanistically, the 3 SNPs regulated estrogen receptor-dependant LY75 and GPR160 expression. LY75 suppression induced epithelial-to-mesenchymal transition (EMT) in breast cancer cell lines, accompanied by increased migratory capacity in vitro. LY75 knockdown also resulted in predominant downregulation of functional pathways such as cell proliferation, while pathways associated with mesenchymal stimulation were generally increased. GPR160 knockdown also resulted in downregulation of cell proliferation pathways. Conclusions: This SNP genotype and AI treatment interaction clinical study revealed unique genetic variants that differentiate anastrozole and exemestane efficacy. The signals were lost in the GWAS analysis when anastrozole and exemestane were combined. Preclinical laboratory studies revealed novel functions of LY75 and GPR160 in breast cancer. These findings represent potential steps towards individualized AI therapy.
Citation Format: Junmei Cairns, James N. Ingle, Krishna R. Kalari, Lois E. Shepherd, Matthew J. Ellis, Paul E. Goss, Poulami Barman, Erin E. Carlson, Matthew P. Goetz, Richard M. Weinshilboum, Liewei Wang. The interaction between SNP genotype and aromatase inhibitor treatment response in early breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-103.
Collapse
|
29
|
Marshall AP, Shirley JD, Carlson EE. Enzyme-targeted fluorescent small-molecule probes for bacterial imaging. Curr Opin Chem Biol 2020; 57:155-165. [PMID: 32799037 DOI: 10.1016/j.cbpa.2020.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 01/12/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/26/2022]
Abstract
Molecular imaging methods to visualize myriad biochemical processes in bacteria have traditionally been dependent upon molecular biology techniques to incorporate fluorescent biomolecules (e.g., fusion proteins). Such methods have been instrumental in our understanding of how bacteria function but are not without drawbacks, including potential perturbation to native protein expression and function. To overcome these limitations, the use of fluorescent small-molecule probes has gained much attention. Here, we highlight examples from the recent literature that showcase the utility of small-molecule probes for the fluorescence imaging of bacterial cells, including electrophilic, metabolic, and enzyme-activated probes. Although the use of these types of compounds for bacterial imaging is still relatively new, the selected examples demonstrate the exciting potential of these critical tools in the exploration of bacterial physiology.
Collapse
Affiliation(s)
- Andrew P Marshall
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
| |
Collapse
|
30
|
Espinasse A, Wen X, Goodpaster JD, Carlson EE. Mechanistic Studies of Bioorthogonal ATP Analogues for Assessment of Histidine Kinase Autophosphorylation. ACS Chem Biol 2020; 15:1252-1260. [PMID: 32043868 DOI: 10.1021/acschembio.9b01024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Phosphorylation is an essential protein modification and is most commonly associated with hydroxyl-containing amino acids via an adenosine triphosphate (ATP) substrate. The last decades have brought greater appreciation to the roles that phosphorylation of myriad amino acids plays in biological signaling, metabolism, and gene transcription. Histidine phosphorylation occurs in both eukaryotes and prokaryotes but has been shown to dominate signaling networks in the latter due to its role in microbial two-component systems. Methods to investigate histidine phosphorylation have lagged behind those to study serine, threonine, and tyrosine modifications due to its inherent instability and the historical view that this protein modification was rare. An important strategy to overcome the reactivity of phosphohistidine is the development of substrate-based probes with altered chemical properties that improve modification longevity but that do not suffer from poor recognition or transfer by the protein. Here, we present combined experimental and computational studies to better understand the molecular requirements for efficient histidine phosphorylation by comparison of the native kinase substrate, ATP, and alkylated ATP derivatives. While recognition of the substrates by the histidine kinases is an important parameter for the formation of phosphohistidine derivatives, reaction sterics also affect the outcome. In addition, we found that stability of the resulting phosphohistidine moieties correlates with the stability of their hydrolysis products, specifically with their free energy in solution. Interestingly, alkylation dramatically affects the stability of the phosphohistidine derivatives at very acidic pH values. These results provide critical mechanistic insights into histidine phosphorylation and will facilitate the design of future probes to study enzymatic histidine phosphorylation.
Collapse
Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Xuelan Wen
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States
| |
Collapse
|
31
|
Sharifzadeh S, Dempwolff F, Kearns DB, Carlson EE. Harnessing β-Lactam Antibiotics for Illumination of the Activity of Penicillin-Binding Proteins in Bacillus subtilis. ACS Chem Biol 2020; 15:1242-1251. [PMID: 32155044 DOI: 10.1021/acschembio.9b00977] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Selective chemical probes enable individual investigation of penicillin-binding proteins (PBPs) and provide critical information about their enzymatic activity with spatial and temporal resolution. To identify scaffolds for novel probes to study peptidoglycan biosynthesis in Bacillus subtilis, we evaluated the PBP inhibition profiles of 21 β-lactam antibiotics from different structural subclasses using a fluorescence-based assay. Most compounds readily labeled PBP1, PBP2a, PBP2b, or PBP4. Almost all penicillin scaffolds were coselective for all or combinations of PBP2a, 2b, and 4. Cephalosporins, on the other hand, possessed the lowest IC50 values for PBP1 alone or along with PBP4 (ceftriaxone, cefoxitin) and 2b (cefotaxime) or 2a, 2b, and 4 (cephalothin). Overall, five selective inhibitors for PBP1 (aztreonam, faropenem, piperacillin, cefuroxime, and cefsulodin), one selective inhibitor for PBP5 (6-aminopenicillanic acid), and various coselective inhibitors for other PBPs in B. subtilis were discovered. Surprisingly, carbapenems strongly inhibited PBP3, formerly shown to have low affinity for β-lactams and speculated to be involved in β-lactam resistance in B. subtilis. To investigate the specific roles of PBP3, we developed activity-based probes based on the meropenem core and utilized them to monitor the activity of PBP3 in living cells. We showed that PBP3 activity localizes as patches in single cells and concentrates as a ring at the septum and the division site during the cell growth cycle. Our activity-based approach enabled spatial resolution of the transpeptidation activity of individual PBPs in this model microorganism, which was not possible with previous chemical and biological approaches.
Collapse
Affiliation(s)
| | - Felix Dempwolff
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | | |
Collapse
|
32
|
Kiessling LL, Carlson EE. Advancing Chemical Microbiology. ACS Chem Biol 2020; 15:1115-1118. [PMID: 32408751 DOI: 10.1021/acschembio.0c00330] [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]
|
33
|
Sharifzadeh S, Brown NW, Shirley JD, Bruce KE, Winkler ME, Carlson EE. Chemical tools for selective activity profiling of bacterial penicillin-binding proteins. Methods Enzymol 2020; 638:27-55. [PMID: 32416917 DOI: 10.1016/bs.mie.2020.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 12/13/2022]
Abstract
Penicillin-binding proteins (PBPs) are membrane-associated proteins involved in the biosynthesis of peptidoglycan (PG), the main component of bacterial cell walls. These proteins were discovered and named for their affinity to bind the β-lactam antibiotic penicillin. The importance of the PBPs has long been appreciated; however, specific roles of individual family members in each bacterial strain, as well as their protein-protein interactions, are yet to be understood. The apparent functional redundancy of the 4-18 PBPs that most eubacteria possess makes determination of their individual roles difficult. Existing techniques to study PBPs are not ideal because they do not directly visualize protein activity and can suffer from artifacts and perturbations of native PBP function. Therefore, development of new methods for studying the roles of individual PBPs in cell wall synthesis is required. We recently generated a library of fluorescent chemical probes containing a β-lactone scaffold that specifically targets the PBPs, enabling the visualization of their catalytic activity. Herein, we describe a general protocol to label and detect the activity of individual PBPs in Streptococcus pneumoniae using our fluorescent β-lactone probes.
Collapse
Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Nathaniel W Brown
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Kevin E Bruce
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Malcolm E Winkler
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
| |
Collapse
|
34
|
Thielen MK, Carlson EE, May JF. Discovery of small molecules that sensitize
Salmonella
to polymyxin antibiotics. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
35
|
Ingle JN, Cairns J, Suman VJ, Shepherd LE, Fasching PA, Hoskin TL, Singh RJ, Desta Z, Kalari KR, Ellis MJ, Goss PE, Chen BE, Volz B, Barman P, Carlson EE, Haddad T, Goetz MP, Goodnature B, Cuellar ME, Walters MA, Correia C, Kaufmann SH, Weinshilboum RM, Wang L. Anastrozole has an Association between Degree of Estrogen Suppression and Outcomes in Early Breast Cancer and is a Ligand for Estrogen Receptor α. Clin Cancer Res 2020; 26:2986-2996. [PMID: 32098767 DOI: 10.1158/1078-0432.ccr-19-3091] [Citation(s) in RCA: 11] [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] [Received: 09/19/2019] [Revised: 01/07/2020] [Accepted: 02/21/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE To determine if the degree of estrogen suppression with aromatase inhibitors (AI: anastrozole, exemestane, letrozole) is associated with efficacy in early-stage breast cancer, and to examine for differences in the mechanism of action between the three AIs. EXPERIMENTAL DESIGN Matched case-control studies [247 matched sets from MA.27 (anastrozole vs. exemestane) and PreFace (letrozole) trials] were undertaken to assess whether estrone (E1) or estradiol (E2) concentrations after 6 months of adjuvant therapy were associated with risk of an early breast cancer event (EBCE). Preclinical laboratory studies included luciferase activity, cell proliferation, radio-labeled ligand estrogen receptor binding, surface plasmon resonance ligand receptor binding, and nuclear magnetic resonance assays. RESULTS Women with E1 ≥1.3 pg/mL and E2 ≥0.5 pg/mL after 6 months of AI treatment had a 2.2-fold increase in risk (P = 0.0005) of an EBCE, and in the anastrozole subgroup, the increase in risk of an EBCE was 3.0-fold (P = 0.001). Preclinical laboratory studies examined mechanisms of action in addition to aromatase inhibition and showed that only anastrozole could directly bind to estrogen receptor α (ERα), activate estrogen response element-dependent transcription, and stimulate growth of an aromatase-deficient CYP19A1-/- T47D breast cancer cell line. CONCLUSIONS This matched case-control clinical study revealed that levels of estrone and estradiol above identified thresholds after 6 months of adjuvant anastrozole treatment were associated with increased risk of an EBCE. Preclinical laboratory studies revealed that anastrozole, but not exemestane or letrozole, is a ligand for ERα. These findings represent potential steps towards individualized anastrozole therapy.
Collapse
Affiliation(s)
- James N Ingle
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota.
| | - Junmei Cairns
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Vera J Suman
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | | | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital, Erlangen, Germany
| | - Tanya L Hoskin
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Ravinder J Singh
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Zeruesenay Desta
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Krishna R Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Matthew J Ellis
- Department of Medicine, Baylor University College of Medicine, Houston, Texas
| | - Paul E Goss
- Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts
| | | | - Bernhard Volz
- Department of Business Informatics, University of Applied Sciences Ansbach, Ansbach, Germany
| | - Poulami Barman
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Erin E Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Tufia Haddad
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Goetz
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Barbara Goodnature
- Patient advocate, Mayo Clinic Breast Cancer Specialized Program of Research Excellence, Rochester, Minnesota
| | - Matthew E Cuellar
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota
| | - Cristina Correia
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Scott H Kaufmann
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Division of Oncology Research, Mayo Clinic, Rochester, Minnesota
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
36
|
Marshall AP, Johnson AR, Vega MM, Thomson RJ, Carlson EE. Ion Mobility Mass Spectrometry as an Efficient Tool for Identification of Streptorubin B in Streptomyces coelicolor M145. J Nat Prod 2020; 83:159-163. [PMID: 31904955 PMCID: PMC7045693 DOI: 10.1021/acs.jnatprod.9b00828] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ion mobility spectrometry was utilized to corroborate the identity of streptorubin B (2) as the natural product produced by Streptomyces coelicolor. Natural product 2 was initially assigned as butylcycloheptylprodigiosin (3), and only relatively recently was this assignment clarified. We present additional evidence of this assignment by comparing collisional cross sections (Ω) of synthetic standards of 2, 3, and metacycloprodigiosin (4) to the cyclic prodiginine produced by S. coelicolor. Calculated theoretical Ω values demonstrate that cyclic prodiginines could be identified without standards. This work highlights ion mobility as an efficient tool for the dereplication of natural products.
Collapse
Affiliation(s)
- Andrew P. Marshall
- Department of Chemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Andrew R. Johnson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Marvin M. Vega
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Erin E. Carlson
- Department of Chemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Corresponding Author:
| |
Collapse
|
37
|
Mitchell SL, Hudson-Smith NV, Cahill MS, Reynolds BN, Frand SD, Green CM, Wang C, Hang MN, Hernandez RT, Hamers RJ, Feng ZV, Haynes CL, Carlson EE. Chronic exposure to complex metal oxide nanoparticles elicits rapid resistance in Shewanella oneidensis MR-1. Chem Sci 2019; 10:9768-9781. [PMID: 32055346 PMCID: PMC6993611 DOI: 10.1039/c9sc01942a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 04/19/2019] [Accepted: 08/29/2019] [Indexed: 12/20/2022] Open
Abstract
Engineered nanoparticles are incorporated into numerous emerging technologies because of their unique physical and chemical properties. Many of these properties facilitate novel interactions, including both intentional and accidental effects on biological systems. Silver-containing particles are widely used as antimicrobial agents and recent evidence indicates that bacteria rapidly become resistant to these nanoparticles. Much less studied is the chronic exposure of bacteria to particles that were not designed to interact with microorganisms. For example, previous work has demonstrated that the lithium intercalated battery cathode nanosheet, nickel manganese cobalt oxide (NMC), is cytotoxic and causes a significant delay in growth of Shewanella oneidensis MR-1 upon acute exposure. Here, we report that S. oneidensis MR-1 rapidly adapts to chronic NMC exposure and is subsequently able to survive in much higher concentrations of these particles, providing the first evidence of permanent bacterial resistance following exposure to nanoparticles that were not intended as antibacterial agents. We also found that when NMC-adapted bacteria were subjected to only the metal ions released from this material, their specific growth rates were higher than when exposed to the nanoparticle. As such, we provide here the first demonstration of bacterial resistance to complex metal oxide nanoparticles with an adaptation mechanism that cannot be fully explained by multi-metal adaptation. Importantly, this adaptation persists even after the organism has been grown in pristine media for multiple generations, indicating that S. oneidensis MR-1 has developed permanent resistance to NMC.
Collapse
Affiliation(s)
- Stephanie L Mitchell
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
| | - Natalie V Hudson-Smith
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
| | - Meghan S Cahill
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
| | - Benjamin N Reynolds
- Department of Biochemistry, Molecular Biology, and Biophysics , University of Minnesota , 321 Church Street SE , Minneapolis , Minnesota 55454 , USA
| | - Seth D Frand
- Chemistry Department , Augsburg University , 2211 Riverside Ave , Minneapolis , MN 55454 , USA
| | - Curtis M Green
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Chenyu Wang
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Mimi N Hang
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Rodrigo Tapia Hernandez
- Chemistry Department , Augsburg University , 2211 Riverside Ave , Minneapolis , MN 55454 , USA
| | - Robert J Hamers
- Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , WI 53706 , USA
| | - Z Vivian Feng
- Chemistry Department , Augsburg University , 2211 Riverside Ave , Minneapolis , MN 55454 , USA
| | - Christy L Haynes
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
| | - Erin E Carlson
- Department of Chemistry , University of Minnesota , 207 Pleasant St. SE , Minneapolis , MN 55455 , USA .
- Department of Biochemistry, Molecular Biology, and Biophysics , University of Minnesota , 321 Church Street SE , Minneapolis , Minnesota 55454 , USA
- Department of Medicinal Chemistry , University of Minnesota , 208 Harvard Street SE , Minneapolis , 55454 , USA
| |
Collapse
|
38
|
Kalari KR, Sinnwell JP, Thompson KJ, Tang X, Carlson EE, Yu J, Vedell PT, Ingle JN, Weinshilboum RM, Boughey JC, Wang L, Goetz MP, Suman V. PANOPLY: Omics-Guided Drug Prioritization Method Tailored to an Individual Patient. JCO Clin Cancer Inform 2019; 2:1-11. [PMID: 30652605 DOI: 10.1200/cci.18.00012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The majority of patients with cancer receive treatments that are minimally informed by omics data. We propose a precision medicine computational framework, PANOPLY (Precision Cancer Genomic Report: Single Sample Inventory), to identify and prioritize drug targets and cancer therapy regimens. MATERIALS AND METHODS The PANOPLY approach integrates clinical data with germline and somatic features obtained from multiomics platforms and applies machine learning and network analysis approaches in the context of the individual patient and matched controls. The PANOPLY workflow uses the following four steps: selection of matched controls to the patient of interest; identification of patient-specific genomic events; identification of suitable drugs using the driver-gene network and random forest analyses; and provision of an integrated multiomics case report of the patient with prioritization of anticancer drugs. RESULTS The PANOPLY workflow can be executed on a stand-alone virtual machine and is also available for download as an R package. We applied the method to an institutional breast cancer neoadjuvant chemotherapy study that collected clinical and genomic data as well as patient-derived xenografts to investigate the prioritization offered by PANOPLY. In a chemotherapy-resistant patient-derived xenograft model, we found that that the prioritized drug, olaparib, was more effective than placebo in treating the tumor ( P < .05). We also applied PANOPLY to in-house and publicly accessible multiomics tumor data sets with therapeutic response or survival data available. CONCLUSION PANOPLY shows promise as a means to prioritize drugs on the basis of clinical and multiomics data for an individual patient with cancer. Additional studies are needed to confirm this approach.
Collapse
Affiliation(s)
| | | | | | | | | | - Jia Yu
- All authors: Mayo Clinic, Rochester, MN
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Johnson AR, Carlson EE. Structure Elucidation of Macrolide Antibiotics Using MS n Analysis and Deuterium Labelling. J Am Soc Mass Spectrom 2019; 30:1464-1480. [PMID: 30993640 DOI: 10.1007/s13361-019-02210-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/28/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
The 14- and 16-membered macrolide antibiotics are an important structural class. Ubiquitously produced by a number of bacterial strains, namely actinomycetes, purification and structure elucidation of the wide array of analogs is challenging, both for discovery efforts and methodologies to monitor for byproducts, metabolites, and contaminants. Collision-induced dissociation mass spectrometry offers an attractive solution, enabling characterization of mixtures, and providing a wealth of structural information. However, interpretation of these spectra can be difficult. We present a study of 14- and 16-membered macrolide antibiotics, including MSn analysis for unprecedented depth of coverage, and complimentary analysis with D2O and H218O labeling to elucidate fragmentation mechanisms. These analyses contrast the behaviors of varying classes of macrolides and highlight how analogues can be identified in relation to similar structures, which will provide utility for future studies of novel macrolides, as well as impurities, metabolites, and degradation products of pharmaceuticals. Graphical Abstract.
Collapse
Affiliation(s)
- Andrew R Johnson
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Erin E Carlson
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA.
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN, 55455, USA.
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA.
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
| |
Collapse
|
40
|
Kocaoglu O, Calvo RA, Sham LT, Cozy LM, Lanning BR, Francis S, Winkler ME, Kearns DB, Carlson EE. Selective Penicillin-Binding Protein Imaging Probes Reveal Substructure in Bacterial Cell Division. ACS Chem Biol 2019; 14:1672. [PMID: 31265231 DOI: 10.1021/acschembio.9b00459] [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]
|
41
|
Tollefson EJ, Allen CR, Chong G, Zhang X, Rozanov ND, Bautista A, Cerda JJ, Pedersen JA, Murphy CJ, Carlson EE, Hernandez R. Preferential Binding of Cytochrome c to Anionic Ligand-Coated Gold Nanoparticles: A Complementary Computational and Experimental Approach. ACS Nano 2019; 13:6856-6866. [PMID: 31082259 DOI: 10.1021/acsnano.9b01622] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Membrane-bound proteins can play a role in the binding of anionic gold nanoparticles (AuNPs) to model bilayers; however, the mechanism for this binding remains unresolved. In this work, we determine the relative orientation of the peripheral membrane protein cytochrome c in binding to a mercaptopropionic acid-functionalized AuNP (MPA-AuNP). As this is nonrigid binding, traditional methods involving crystallographic or rigid molecular docking techniques are ineffective at resolving the question. Instead, we have implemented a computational assay technique using a cross-correlation of a small ensemble of 200 ns long molecular dynamics trajectories to identify a preferred nonrigid binding orientation or pose of cytochrome c on MPA-AuNPs. We have also employed a mass spectrometry-based footprinting method that enables the characterization of the stable protein corona that forms at long time-scales in solution but remains in a dynamic state. Through the combination of these computational and experimental primary results, we have established a consensus result establishing the identity of the exposed regions of cytochrome c in proximity to MPA-AuNPs and its complementary pose(s) with amino-acid specificity. Moreover, the tandem use of the two methods can be applied broadly to determine the accessibility of membrane-binding sites for peripheral membrane proteins upon adsorption to AuNPs or to determine the exposed amino-acid residues of the hard corona that drive the acquisition of dynamic soft coronas. We anticipate that the combined use of simulation and experimental methods to characterize biomolecule-nanoparticle interactions, as demonstrated here, will become increasingly necessary as the complexity of such target systems grows.
Collapse
Affiliation(s)
- Emily J Tollefson
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Caley R Allen
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Gene Chong
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Xi Zhang
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Nikita D Rozanov
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Anthony Bautista
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Jennifer J Cerda
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Joel A Pedersen
- Environmental Chemistry and Technology Program , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Catherine J Murphy
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Erin E Carlson
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Rigoberto Hernandez
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| |
Collapse
|
42
|
Gehrke EJ, Zhang X, Pimentel-Elardo SM, Johnson AR, Rees CA, Jones SE, Hindra, Gehrke SS, Turvey S, Boursalie S, Hill JE, Carlson EE, Nodwell JR, Elliot MA. Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2. eLife 2019; 8:47691. [PMID: 31215866 PMCID: PMC6584129 DOI: 10.7554/elife.47691] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [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: 04/14/2019] [Accepted: 06/04/2019] [Indexed: 12/17/2022] Open
Abstract
Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces’ arsenal of signaling and antagonistic compounds.
Collapse
Affiliation(s)
- Emma J Gehrke
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Xiafei Zhang
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | | | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | - Christiaan A Rees
- Geisel School of Medicine and Thayer School of Engineering, Dartmouth College, Hanover, United States
| | - Stephanie E Jones
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Hindra
- Department of Biology, McMaster University, Hamilton, Canada
| | - Sebastian S Gehrke
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Sonya Turvey
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Suzanne Boursalie
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Jane E Hill
- Geisel School of Medicine and Thayer School of Engineering, Dartmouth College, Hanover, United States
| | - Erin E Carlson
- Department of Chemistry, Indiana University, Bloomington, United States.,Department of Chemistry, University of Minnesota, Minneapolis, United States
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Marie A Elliot
- Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| |
Collapse
|
43
|
Dudenkov TM, Liu D, Cairns J, Devarajan S, Zhuang Y, Ingle JN, Buzdar AU, Robson ME, Kubo M, Batzler A, Barman P, Jenkins GD, Carlson EE, Goetz MP, Northfelt DW, Moreno-Aspitia A, Desta Z, Reid JM, Kalari KR, Wang L, Weinshilboum RM. Anastrozole Aromatase Inhibitor Plasma Drug Concentration Genome-Wide Association Study: Functional Epistatic Interaction Between SLC38A7 and ALPPL2. Clin Pharmacol Ther 2019; 106:219-227. [PMID: 30648747 PMCID: PMC6612579 DOI: 10.1002/cpt.1359] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/13/2018] [Indexed: 01/13/2023]
Abstract
Anastrozole is a widely prescribed aromatase inhibitor for the therapy of estrogen receptor positive (ER+) breast cancer. We performed a genome‐wide association study (GWAS) for plasma anastrozole concentrations in 687 postmenopausal women with ER+ breast cancer. The top single‐nucleotide polymorphism (SNP) signal mapped across SLC38A7 (rs11648166, P = 2.3E‐08), which we showed to encode an anastrozole influx transporter. The second most significant signal (rs28845026, P = 5.4E‐08) mapped near ALPPL2 and displayed epistasis with the SLC38A7 signal. Both of these SNPs were cis expression quantitative trait loci (eQTL)s for these genes, and patients homozygous for variant genotypes for both SNPs had the highest drug concentrations, the highest SLC38A7 expression, and the lowest ALPPL2 expression. In summary, our GWAS identified a novel gene encoding an anastrozole transporter, SLC38A7, as well as epistatic interaction between SNPs in that gene and SNPs near ALPPL2 that influenced both the expression of the transporter and anastrozole plasma concentrations.
Collapse
Affiliation(s)
- Tanda M Dudenkov
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Junmei Cairns
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Sandhya Devarajan
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Yongxian Zhuang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - James N Ingle
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Aman U Buzdar
- Department of Breast Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark E Robson
- Breast Medicine Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Japan
| | - Anthony Batzler
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Poulami Barman
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Gregory D Jenkins
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Erin E Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew P Goetz
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Donald W Northfelt
- Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Scottsdale, Arizona, USA
| | - Alvaro Moreno-Aspitia
- Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Zeruesenay Desta
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Joel M Reid
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Krishna R Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
44
|
Thompson KJ, Alaparthi T, Sinnwell JP, Carlson EE, Tang X, Bockol M, Vedell PT, Ingle JN, Suman V, Weinshilboum RM, Wang L, Boughey JC, Kalari KR, Goetz MP. Abstract P1-03-04: Molecular subtyping of androgen receptor-positive patients using gene expression profiles. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p1-03-04] [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
Breast cancer is a heterogeneous disease, and unsupervised clustering approaches using gene expression data have identified 3-6 distinct subtypes of triple negative breast cancer (TNBC). A genomically and clinically distinct subtype of TNBC is referred to as LAR (Luminal Androgen Receptor). Tumors with this subtype typically express high levels of the AR and exhibit alterations within genes involved in the PI3K pathway (e.g. PIK3CA mutations). Prospective studies are underway using drugs that target the AR alone or in combination with PI3K and CDK 4/6 inhibitors. Given the importance of accurately identifying this subtype, we sought to develop an online tool that uses submitted gene expression data to confidently characterize LAR samples by corroborating the classification with previously published clustering approaches.
Methods: We have investigated TNBC RNA-Seq data from The Cancer Genome Atlas (TCGA) breast cancer study (N=123 samples) by cluster analysis. Analysis of the average silhouette width in both biased and unbiased K-means clustering approaches demonstrated LAR and basal as two distinct and significant clusters. A shrunken centroid model of 426 differentially expressed genes, named as CABAL (Clustering Among BAsal and Luminal androgen receptor), was constructed by comparing LAR and basal subtypes.
Results: We applied the CABAL model to classify the four TNBC microarray datasets that were previously used in clustering experiments as well as an independent RNA-Seq data cohort. Non-negative matrix factorization (NMF) and fuzzy clustering were applied to the samples (N=1046). Clustering similarity among the methods was assessed with the adjusted rand index, and CABAL demonstrated significant similarity with both fuzzy and NMF clustering methods. Similarly, hierarchical clustering analysis performed on the pooled cohort of 1046 samples recapitulated the CABAL classification with an area under the receiver operating curve of 0.91.
Conclusions: Confident and robust identification of samples with the LAR phenotype is paramount in the assessment of clinical associations and therapeutic efficacy. To facilitate LAR identification, we have provided a web-based prediction tool of the CABAL classification, integrated with the NMF and fuzzy clustering results to identify candidate LAR samples. The end user is provided with the pair-wise adjusted rand indexes, thus reinforcing in the clustering characterizations. Further, our online LAR depiction tool provides a set of graphical and tabular summaries, which will be illustrated, while providing additional molecular characterizations of the PAM50 and Metabric classifications. The availability of this tool could advance the genomic research and treatment of TNBC patients.
Citation Format: Thompson KJ, Alaparthi T, Sinnwell JP, Carlson EE, Tang X, Bockol M, Vedell PT, Ingle JN, Suman V, Weinshilboum RM, Wang L, Boughey JC, Kalari KR, Goetz MP. Molecular subtyping of androgen receptor-positive patients using gene expression profiles [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-03-04.
Collapse
Affiliation(s)
| | | | | | | | - X Tang
- Mayo Clinic, Rochester, MN
| | | | | | | | | | | | - L Wang
- Mayo Clinic, Rochester, MN
| | | | | | | |
Collapse
|
45
|
Kalari KR, Sinnwell JP, Thompson KJ, Tang X, Carlson EE, Alaparthi T, Yu J, Vedell PT, Kalmbach MT, Bockol MA, Hossain A, Weinshilboum RM, Boughey JC, Wang L, Suman VJ, Goetz MP. Abstract P3-06-10: Multiscale modeling of omics data for precision breast cancer treatment. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p3-06-10] [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
Introduction: The vast majority of cancer patients continue to receive treatments that are minimally informed by omics data. In the case of breast cancer, only ER and HER2 are routinely used for treatment selection. There is a particular need for personalized treatment in individuals with primary and secondary drug resistance or aggressive breast cancers. Emerging bioinformatics and statistical methods have made a fundamental impact on cancer research. However, challenges remains with regard to patient-centric data analysis and providing genomic data guidance to oncologists. There exists a large number of FDA approved anti-neoplastic drugs used to treat cancers other than breast and the development of innovative informatics methods and algorithms to repurpose those drugs should benefit breast cancer patients.
Methods and Results: We have developed precision care systems (such as PANOPLY and CORPUS) to identify personalized therapies for an individual patient and to deliver genomic reports in a standard, searchable format so that a researcher or an oncologist can quickly navigate through molecular data and obtain prioritized drugs and targets.The PANOPLY (Precision cancer genomics report: single sample inventory) algorithm applies machine learning and topology-based network analysis methods to integrate multi-omics profiles and clinical data; individual-specific molecular alterations are identified and compared with a set of matched-controls having similar clinical data. Since there is a lack of a “gold standard” dataset to test such algorithms, we simulated 500 case-control sets and evaluated drug predictions across multiple simulation scenarios. We applied the PANOPLY algorithm to The Cancer Genome Atlas (TCGA) breast cancer cohort, which consists of multi-omics data and clinical data. In addition, PANOPLY was also applied to an in-house neoadjuvant breast cancer study (BEAUTY) that consists of multi-omics data, clinical data, and patient-derived xenografts (PDXs). In the TCGA breast cancer study we obtained survival data to determine the cases and matched-controls; and in the BEAUTY, we used pathologic complete response (pCR) as an outcome to determine responders and non-responders. Recurrent targetable alterations were not enriched in patients without pCR in the BEAUTY study. We have applied the PANOPLY to non-responder patients to identify individual specific alterations, dysregulated networks, drug targets, and drugs for each patient and stored them as case reports in CORPUS (Computational Oncology Reports and Precision therapeUticS), a web-based repository that allows clinicians to review genomic reports. Using comprehensive “omic” data derived from a triple negative breast cancer patient who had pre and post-neoadjuvant chemotherapy PDXs, PANOPLY prioritized the PARP inhibitors as the top class of drug. Using the PDX models available from this patient, we tested olaparib and confirmed the in vivo antitumor activity (more effective than vehicle with a p-value < 0.05 in the PDXs). Further studies to confirm PANOPLY findings are currently underway.
Conclusions: In summary, the PANOPLY and CORPUS systems incorporate molecular data together with clinical data to provide genomic reports with proposed drug targets to advance or enable precision breast cancer care.
Citation Format: Kalari KR, Sinnwell JP, Thompson KJ, Tang X, Carlson EE, Alaparthi T, Yu J, Vedell PT, Kalmbach MT, Bockol MA, Hossain A, Weinshilboum RM, Boughey JC, Wang L, Suman VJ, Goetz MP. Multiscale modeling of omics data for precision breast cancer treatment [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-10.
Collapse
Affiliation(s)
| | | | | | - X Tang
- Mayo Clinic, Rochester, MN
| | | | | | - J Yu
- Mayo Clinic, Rochester, MN
| | | | | | | | | | | | | | - L Wang
- Mayo Clinic, Rochester, MN
| | | | | |
Collapse
|
46
|
Feng ZV, Miller BR, Linn TG, Pho T, Hoang KNL, Hang MN, Mitchell SL, Hernandez RT, Carlson EE, Hamers RJ. Biological impact of nanoscale lithium intercalating complex metal oxides to model bacterium B. subtilis. Environ Sci Nano 2019; 6:305-314. [PMID: 31572614 PMCID: PMC6768416 DOI: 10.1039/c8en00995c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The wide applications of lithium intercalating complex metal oxides in energy storage devices call for a better understanding of their environmental impact at the end of their life cycle. In this study, we examine the biological impact of a panel of nanoscale lithium nickel manganese cobalt oxides (Li x Ni y Mn z Co1-y-z O2, 0 < x, y, z < 1, abbreviated to NMCs) to a model Gram-positive bacterium, Bacillus subtilis, in terms of cellular respiration and growth. A highly sensitive single-cell gel electrophoresis method is also applied for the first time to understand the genotoxicity of these nanomaterials to bacterial cells. Results from these assays indicate that the free Ni and Co ions released from the incongruent dissolution of the NMC material in B. subtilis growth medium induced both hindered growth and cellular respiration. More remarkably, the DNA damage induced by the combination of the two ions in solution is comparable to that induced by the NMC material, which suggests that the free Ni and Co ions are responsible for the toxicity observed. A material redesign by enriching Mn is also presented. The combined approaches of evaluating their impact on bacterial growth, respiration, and DNA damage at a single-cell level, as well as other phenotypical changes allows us to probe the nanomaterials and bacterial cells from a mechanistic prospective, and provides a useful means to an understanding of bacterial response to new potential environmental stressors.
Collapse
Affiliation(s)
- Z. Vivian Feng
- Chemistry Department, Augsburg University, Minneapolis, MN 55454, USA
| | - Blake R. Miller
- Chemistry Department, Augsburg University, Minneapolis, MN 55454, USA
| | - Taylor G. Linn
- Chemistry Department, Augsburg University, Minneapolis, MN 55454, USA
| | - Thomas Pho
- Chemistry Department, Augsburg University, Minneapolis, MN 55454, USA
| | | | - Mimi N. Hang
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | | | | | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J. Hamers
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| |
Collapse
|
47
|
Abstract
Nanoparticles have exceptional properties that make them outstanding candidates for improving diagnostics and the treatment of infectious disease. Their small size, distinctive intrinsic properties, and ability to be decorated with a variety of complex functionalities make them uniquely capable of detection and targeting of certain diseases. Nanotechnology has the ability to increase the sensitivity of detection methods, the potency and ease of treatment, and the effectiveness of vaccinations. However, major challenges remain to their application in low-resource settings due in large part to the sensitivity of these particles to their local environment, a property that makes them both exceptional for detection and prone to complications or failure during synthesis and utilization. These challenges are likely to be solved only by continued and enhanced communication across scientific disciplines, for example, medical doctors and diagnosticians providing information about what is needed in new technologies. This information will enable materials scientists and engineers to rapidly address the corresponding technical challenges, such as the scalable and reproducible generation of nontoxic and stable, yet responsible nanoparticles.
Collapse
Affiliation(s)
- Stephanie L. Mitchell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55454, United States
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55454, United States
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
48
|
Chase OM, Espinasse A, Wilke KE, Carlson EE. Exploration of the Effects of γ-Phosphate-Modified ATP Analogues on Histidine Kinase Autophosphorylation. Biochemistry 2018; 57:4368-4373. [PMID: 29944360 DOI: 10.1021/acs.biochem.8b00485] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
While two-component systems (TCSs), composed of a sensor histidine kinase (HK) and a response regulator, are the main signaling pathways in bacteria, global TCS activity remains poorly described. Here, we report the kinetic parameters of the HK autophosphorylation reaction using previously uncharacterized γ-phosphate-modified ATP analogues to further elucidate their utility as activity-based probes for global TCS analysis. Given the increased stability of thiophosphorylated histidine in comparison to that of the native phosphoryl modification, which is attributed to the decreased electrophilicity of this moiety, we anticipated that ATPγS may be turned over much more slowly by the HKs. Surprisingly, we found this not to be the case, with the turnover numbers decreasing <1 order of magnitude. Instead, we found that alkylation of the thiophosphate had a much more dramatic effect on turnover and, in one case, the binding affinity of this substrate analogue (BODIPY-FL-ATPγS).
Collapse
Affiliation(s)
- Olivia M Chase
- Department of Chemistry , University of Minnesota , 207 Pleasant Street Southeast , Minneapolis , Minnesota 55455 , United States
| | - Adeline Espinasse
- Department of Chemistry , University of Minnesota , 207 Pleasant Street Southeast , Minneapolis , Minnesota 55455 , United States
| | - Kaelyn E Wilke
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405 , United States
| | - Erin E Carlson
- Department of Chemistry , University of Minnesota , 207 Pleasant Street Southeast , Minneapolis , Minnesota 55455 , United States.,Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405 , United States.,Department of Medicinal Chemistry , University of Minnesota , 208 Harvard Street Southeast , Minneapolis , Minnesota 55454 , United States.,Department of Biochemistry, Molecular Biology, and Biophysics , University of Minnesota , 321 Church Street Southeast , Minneapolis , Minnesota 55454 , United States
| |
Collapse
|
49
|
Goswami M, Espinasse A, Carlson EE. Disarming the virulence arsenal of Pseudomonas aeruginosa by blocking two-component system signaling. Chem Sci 2018; 9:7332-7337. [PMID: 30542536 PMCID: PMC6237130 DOI: 10.1039/c8sc02496k] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 06/07/2018] [Accepted: 07/06/2018] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas aeruginosa infections have reached a “critical” threat status making novel therapeutic approaches required.
Pseudomonas aeruginosa infections have reached a “critical” threat status making novel therapeutic approaches required. Inhibiting key signaling enzymes known as the histidine kinases (HKs), which are heavily involved with its pathogenicity, has been postulated to be an effective new strategy for treatment. Herein, we demonstrate the potential of this approach with benzothiazole-based HK inhibitors that perturb multiple virulence pathways in the burn wound P. aeruginosa isolate, PA14. Specifically, our compounds significantly reduce the level of toxic metabolites generated by this organism that are involved in quorum-sensing and redox-balancing mechanisms. They also decrease the ability of this organism to swarm and attach to surfaces, likely by influencing their motility appendages. Quantitative transcription analysis of inhibitor-treated cultures showed substantial perturbations to multiple pathways including expression of response regulator GacA, the cognate partner of the “super regulator” of virulence, HK GacS, as well as flagella and pili formation. These promising results establish that blocking of bacterial signaling in P. aeruginosa has dramatic consequences on virulence behaviours, especially in the context of surface-associated infections.
Collapse
Affiliation(s)
- Manibarsha Goswami
- Department of Chemistry , University of Minnesota , 225 Pleasant St. SE , Minneapolis , MN 55454 , USA .
| | - Adeline Espinasse
- Department of Chemistry , University of Minnesota , 225 Pleasant St. SE , Minneapolis , MN 55454 , USA .
| | - Erin E Carlson
- Department of Chemistry , University of Minnesota , 225 Pleasant St. SE , Minneapolis , MN 55454 , USA . .,Department of Medicinal Chemistry , University of Minnesota , USA.,Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , USA
| |
Collapse
|
50
|
Wilke KE, Fihn CA, Carlson EE. Screening serine/threonine and tyrosine kinase inhibitors for histidine kinase inhibition. Bioorg Med Chem 2018; 26:5322-5326. [PMID: 29706527 DOI: 10.1016/j.bmc.2018.04.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022]
Abstract
Histidine kinases of bacterial two-component systems are promising antibacterial targets. Despite their varied, numerous roles, enzymes in the histidine kinase superfamily share a catalytic core that may be exploited to inhibit multiple histidine kinases simultaneously. Characterized by the Bergerat fold, the features of the histidine kinase ATP-binding domain are not found in serine/threonine and tyrosine kinases. However, because each kinase family binds the same ATP substrate, we sought to determine if published serine/threonine and tyrosine kinase inhibitors contained scaffolds that would also inhibit histidine kinases. Using select assays, 222 inhibitors from the Roche Published Kinase Set were screened for binding, deactivation, and aggregation of histidine kinases. Not only do the results of our screen support the distinctions between ATP-binding domains of different kinase families, but the lead molecule identified also presents inspiration for further histidine kinase inhibitor development.
Collapse
Affiliation(s)
- Kaelyn E Wilke
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, United States
| | - Conrad A Fihn
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55455, United States
| | - Erin E Carlson
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, United States; Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55454, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, United States; Department of Molecular and Cellular Biochemistry, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, United States.
| |
Collapse
|