1
|
Davids M, Pooran A, Hermann C, Mottay L, Thompson F, Cardenas J, Gu J, Koeuth T, Meldau R, Limberis J, Gina P, Srivastava S, Calder B, Esmail A, Tomasicchio M, Blackburn J, Gumbo T, Dheda K. A Human Lung Challenge Model to Evaluate the Safety and Immunogenicity of PPD and Live Bacillus Calmette-Guérin. Am J Respir Crit Care Med 2020; 201:1277-1291. [PMID: 31860339 DOI: 10.1164/rccm.201908-1580oc] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rationale: A human model to better understand tuberculosis immunopathogenesis and facilitate vaccine development is urgently needed.Objectives: We evaluated the feasibility, safety, and immunogenicity of live bacillus Calmette-Guérin (BCG) in a lung-oriented controlled human infection model.Methods: We recruited 106 healthy South African participants with varying degrees of tuberculosis susceptibility. Live BCG, sterile PPD, and saline were bronchoscopically instilled into separate lung segments (n = 65). A control group (n = 34) underwent a single bronchoscopy without challenge. The primary outcome was safety. Cellular and antibody immune signatures were identified in BAL before and 3 days after challenge using flow cytometry, ELISA, RNA sequencing, and mass spectrometry.Measurements and Main Results: The frequency of adverse events was low (9.4%; n = 10), similar in the challenge versus control groups (P = 0.8), and all adverse events were mild and managed conservatively in an outpatient setting. The optimal PPD and BCG dose was 0.5 TU and 104 cfu, respectively, based on changes in BAL cellular profiles (P = 0.02) and antibody responses (P = 0.01) at incremental doses before versus after challenge. At 104 versus 103 cfu BCG, there was a significant increase in number of differentially expressed genes (367 vs. 3; P < 0.001) and dysregulated proteins (64 vs. 0; P < 0.001). Immune responses were highly setting specific (in vitro vs. in vivo) and compartment specific (BAL vs. blood) and localized to the challenged lung segments.Conclusions: A lung-oriented mycobacterial controlled human infection model using live BCG and PPD is feasible and safe. These data inform the study of tuberculosis immunopathogenesis and strategies for evaluation and development of tuberculosis vaccine candidates.
Collapse
Affiliation(s)
- Malika Davids
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa
| | - Anil Pooran
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa
| | - Clemens Hermann
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Lynelle Mottay
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa
| | - Fawziyah Thompson
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa
| | - Jacob Cardenas
- Baylor Institute for Immunology Research, Dallas, Texas; and
| | - Jinghua Gu
- Baylor Institute for Immunology Research, Dallas, Texas; and
| | - Thearith Koeuth
- Baylor Institute for Immunology Research, Dallas, Texas; and
| | - Richard Meldau
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa
| | - Jason Limberis
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa
| | - Phindile Gina
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa
| | | | - Bridget Calder
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Aliasgar Esmail
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa
| | - Michele Tomasicchio
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa
| | - Jonathan Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Tawanda Gumbo
- Baylor Institute for Immunology Research, Dallas, Texas; and
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa.,South African Medical Research Council/University of Cape Town Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa.,Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| |
Collapse
|
2
|
Deshpande D, Pasipanodya JG, Srivastava S, Martin KR, Athale S, van Zyl J, Antiabong J, Koeuth T, Lee PS, Dheda K, Gumbo T. Minocycline Immunomodulates via Sonic Hedgehog Signaling and Apoptosis and Has Direct Potency Against Drug-Resistant Tuberculosis. J Infect Dis 2020; 219:975-985. [PMID: 30597040 DOI: 10.1093/infdis/jiy587] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 06/11/2018] [Accepted: 11/14/2018] [Indexed: 11/13/2022] Open
Abstract
Drug-resistant tuberculosis represents a global emergency, requiring new drugs. We found that minocycline was highly potent in laboratory strains of Mycobacterium tuberculosis and that 30 drug-susceptible and multidrug/extensively drug-resistant clinical strains were susceptible to clinically achievable concentrations. In the hollow fiber system model, lung concentration-time profiles of 7 mg/kg/day human-equivalent minocycline dose achieved bacterial kill rates equivalent to those of first-line antituberculosis agents. Minocycline killed extracellular bacilli directly. Minocycline also killed intracellular bacilli indirectly, via concentration-dependent granzyme A-driven apoptosis. Moreover, minocycline demonstrated dose-dependent antiinflammatory activity and downregulation of extracellular matrix-based remodeling pathways and, thus, could protect patients from tuberculosis immunopathology. In RNA sequencing of repetitive samples from the hollow fiber system and in independent protein abundance experiments, minocycline demonstrated dose-dependent inhibition of sonic hedgehog-patched-gli signaling. These findings have implications for improved lung remodeling and for dual immunomodulation and direct microbial kill-based treatment shortening regimens for drug-susceptible and drug-resistant latent and active M. tuberculosis infection.
Collapse
Affiliation(s)
- Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas
| | - Jotam G Pasipanodya
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas
| | - Katherine R Martin
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas
| | - Shruti Athale
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas
| | - Johanna van Zyl
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas
| | - John Antiabong
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas
| | - Thearith Koeuth
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas
| | - Pooi S Lee
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas
| | - Keertan Dheda
- Division of Pulmonology, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, South Africa
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Dallas, Texas.,Division of Pulmonology, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, South Africa
| |
Collapse
|
3
|
Deshpande D, Pasipanodya JG, Srivastava S, Bendet P, Koeuth T, Bhavnani SM, Ambrose PG, Smythe W, McIlleron H, Thwaites G, Gumusboga M, Van Deun A, Gumbo T. Gatifloxacin Pharmacokinetics/Pharmacodynamics-based Optimal Dosing for Pulmonary and Meningeal Multidrug-resistant Tuberculosis. Clin Infect Dis 2019; 67:S274-S283. [PMID: 30496459 DOI: 10.1093/cid/ciy618] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background Gatifloxacin is used for the treatment of multidrug-resistant tuberculosis (MDR-TB). The optimal dose is unknown. Methods We performed a 28-day gatifloxacin hollow-fiber system model of tuberculosis (HFS-TB) study in order to identify the target exposures associated with optimal kill rates and resistance suppression. Monte Carlo experiments (MCE) were used to identify the dose that would achieve the target exposure in 10000 adult patients with meningeal or pulmonary MDR-TB. The optimal doses identified were validated using probit analyses of clinical data from 2 prospective clinical trials of patients with pulmonary and meningeal tuberculosis. Classification and regression-tree (CART) analyses were used to identify the gatifloxacin minimum inhibitory concentration (MIC) below which patients failed or relapsed on combination therapy. Results The target exposure associated with optimal microbial kill rates and resistance suppression in the HFS-TB was a 0-24 hour area under the concentration-time curve-to-MIC of 184. MCE identified an optimal gatifloxacin dose of 800 mg/day for pulmonary and 1200 mg/day for meningeal MDR-TB, and a clinical susceptibility breakpoint of MIC ≤ 0.5 mg/L. In clinical trials, CART identified that 79% patients failed therapy if MIC was >2 mg/L, but 98% were cured if MIC was ≤0.5 mg/L. Probit analysis of clinical data demonstrated a >90% probability of a cure in patients if treated with 800 mg/day for pulmonary tuberculosis and 1200 mg/day for meningeal tuberculosis. Doses ≤400 mg/day were suboptimal. Conclusions Gatifloxacin doses of 800 mg/day and 1200 mg/day are recommended for pulmonary and meningeal MDR-TB treatment, respectively. Gatifloxacin has a susceptible dose-dependent zone at MICs 0.5-2 mg/L.
Collapse
Affiliation(s)
- Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Jotam G Pasipanodya
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Paula Bendet
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Thearith Koeuth
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | - Paul G Ambrose
- Institute for Clinical Pharmacodynamics, Schenectady, New York
| | - Wynand Smythe
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, South Africa
| | - Helen McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, South Africa
| | - Guy Thwaites
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, Churchill Hospital, Oxford, United Kingdom.,Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Armand Van Deun
- Institute of Tropical Medicine, Antwerp, Belgium.,International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| |
Collapse
|
4
|
Deshpande D, Srivastava S, Nuermberger E, Koeuth T, Martin KR, Cirrincione KN, Lee PS, Gumbo T. Multiparameter Responses to Tedizolid Monotherapy and Moxifloxacin Combination Therapy Models of Children With Intracellular Tuberculosis. Clin Infect Dis 2018; 67:S342-S348. [PMID: 30496456 PMCID: PMC6260150 DOI: 10.1093/cid/ciy612] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 01/23/2023] Open
Abstract
Background Children are often neglected during early development of antituberculosis agents, and most receive treatment after it is first tested in adults. However, very young children have tuberculosis that differs in many respects from adult cavitary pneumonia and could have different toxicity profiles to drugs. Linezolid is effective against intracellular tuberculosis, a common manifestation in young children. However, linezolid has considerable toxicity due to inhibition of mitochondrial enzymes. Tedizolid could be a replacement if it shows equal efficacy and reduced toxicity. Methods We performed tedizolid dose-effect studies in the hollow fiber system model of intracellular tuberculosis. We measured linezolid concentrations, colony-forming units (CFU), time-to-positivity, and monocyte viability and performed RNA sequencing on infected cells collected from repetitive sampling of each system. We also compared efficacy of tedizolid vs linezolid and vs tedizolid-moxifloxacin combination. Results There was no downregulation of mitochondrial enzyme genes, with a tedizolid 0-24 hour area under the concentration-time curve (AUC0-24) of up to 90 mg*h/L. Instead, high exposures led to increased mitochondrial gene expression and monocyte survival. The AUC0-24 to minimum inhibitory concentration ratio associated with 80% of maximal bacterial kill (EC80) was 184 by CFU/mL (r2 = 0.96) and 189 by time-to-positivity (r2 = 0.99). Tedizolid EC80 killed 4.0 log10 CFU/mL higher than linezolid EC80. The tedizolid-moxifloxacin combination had a bacterial burden elimination rate constant of 0.27 ± 0.05 per day. Conclusions Tedizolid demonstrated better efficacy than linezolid, without the mitochondrial toxicity gene or cytotoxicity signatures encountered with linezolid. Tedizolid-moxifloxacin combination had a high bacterial elimination rate.
Collapse
Affiliation(s)
- Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Eric Nuermberger
- Center for Tuberculosis Research, Department of Medicine
- Department of International Health, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Thearith Koeuth
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Katherine R Martin
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Kayle N Cirrincione
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Pooi S Lee
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
- Department of Medicine, University of Cape Town, Observatory, South Africa
| |
Collapse
|
5
|
Deshpande D, Alffenaar JWC, Köser CU, Dheda K, Chapagain ML, Simbar N, Schön T, Sturkenboom MGG, McIlleron H, Lee PS, Koeuth T, Mpagama SG, Banu S, Foongladda S, Ogarkov O, Pholwat S, Houpt ER, Heysell SK, Gumbo T. d-Cycloserine Pharmacokinetics/Pharmacodynamics, Susceptibility, and Dosing Implications in Multidrug-resistant Tuberculosis: A Faustian Deal. Clin Infect Dis 2018; 67:S308-S316. [PMID: 30496460 PMCID: PMC6260153 DOI: 10.1093/cid/ciy624] [Citation(s) in RCA: 33] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background d-cycloserine is used to treat multidrug-resistant tuberculosis. Its efficacy, contribution in combination therapy, and best clinical dose are unclear, also data on the d-cycloserine minimum inhibitory concentration (MIC) distributions is scant. Methods We performed a systematic search to identify pharmacokinetic and pharmacodynamic studies performed with d-cycloserine. We then performed a combined exposure-effect and dose fractionation study of d-cycloserine in the hollow fiber system model of tuberculosis (HFS-TB). In parallel, we identified d-cycloserine MICs in 415 clinical Mycobacterium tuberculosis (Mtb) isolates from patients. We utilized these results, including intracavitary concentrations, to identify the clinical dose that would be able to achieve or exceed target exposures in 10000 patients using Monte Carlo experiments (MCEs). Results There were no published d-cycloserine pharmacokinetics/pharmacodynamics studies identified. Therefore, we performed new HFS-TB experiments. Cyloserine killed 6.3 log10 colony-forming units (CFU)/mL extracellular bacilli over 28 days. Efficacy was driven by the percentage of time concentration persisted above MIC (%TMIC), with 1.0 log10 CFU/mL kill achieved by %TMIC = 30% (target exposure). The tentative epidemiological cutoff value with the Sensititre MYCOTB assay was 64 mg/L. In MCEs, 750 mg twice daily achieved target exposure in lung cavities of 92% of patients whereas 500 mg twice daily achieved target exposure in 85% of patients with meningitis. The proposed MCE-derived clinical susceptibility breakpoint at the proposed doses was 64 mg/L. Conclusions Cycloserine is cidal against Mtb. The susceptibility breakpoint is 64 mg/L. However, the doses likely to achieve the cidality in patients are high, and could be neurotoxic.
Collapse
Affiliation(s)
- Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Jan-Willem C Alffenaar
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, United Kingdom
| | - Keertan Dheda
- Lung Immunity Unit, Division of Pulmonology, Department of Medicine, University of Cape Town, Observatory, South Africa
| | - Moti L Chapagain
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Noviana Simbar
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Thomas Schön
- Department of Infectious Diseases and Clinical Microbiology, Kalmar County Hospital
- Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Sweden
| | - Marieke G G Sturkenboom
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Helen McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, South Africa
| | - Pooi S Lee
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Thearith Koeuth
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | - Sayera Banu
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | | | - Oleg Ogarkov
- Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russian Federation
| | - Suporn Pholwat
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Scott K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| |
Collapse
|
6
|
Deshpande D, Pasipanodya JG, Mpagama SG, Srivastava S, Bendet P, Koeuth T, Lee PS, Heysell SK, Gumbo T. Ethionamide Pharmacokinetics/Pharmacodynamics-derived Dose, the Role of MICs in Clinical Outcome, and the Resistance Arrow of Time in Multidrug-resistant Tuberculosis. Clin Infect Dis 2018; 67:S317-S326. [PMID: 30496457 PMCID: PMC6260165 DOI: 10.1093/cid/ciy609] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 01/30/2023] Open
Abstract
Background Ethionamide is used to treat multidrug-resistant tuberculosis (MDR-TB). The antimicrobial pharmacokinetics/pharmacodynamics, the contribution of ethionamide to the multidrug regimen, and events that lead to acquired drug resistance (ADR) are unclear. Methods We performed a multidose hollow fiber system model of tuberculosis (HFS-TB) study to identify the 0-24 hour area under the concentration-time curve (AUC0-24) to minimum inhibitory concentration (MIC) ratios that achieved maximal kill and ADR suppression, defined as target exposures. Ethionamide-resistant isolates underwent whole-genome and targeted Sanger sequencing. We utilized Monte Carlo experiments (MCEs) to identify ethionamide doses that would achieve the target exposures in 10000 patients with pulmonary tuberculosis. We also identified predictors of time-to-sputum conversion in Tanzanian patients on ethionamide- and levofloxacin-based regimens using multivariate adaptive regression splines (MARS). Results An AUC0-24/MIC >56.2 was identified as the target exposure in the HFS-TB. Early efflux pump induction to ethionamide monotherapy led to simultaneous ethambutol and isoniazid ADR, which abrogated microbial kill of an isoniazid-ethambutol-ethionamide regimen. Genome sequencing of isolates that arose during ethionamide monotherapy revealed mutations in both ethA and embA. In MCEs, 20 mg/kg/day achieved the AUC0-24/MIC >56.2 in >95% of patients, provided the Sensititre assay MIC was <2.5 mg/L. In the clinic, MARS revealed that ethionamide Sensititre MIC had linear negative relationships with time-to-sputum conversion until an MIC of 2.5 mg/L, above which patients with MDR-TB failed combination therapy. Conclusions Ethionamide is an important contributor to MDR-TB treatment regimens, at Sensititre MIC <2.5 mg/L. Suboptimal ethionamide exposures led to efflux pump-mediated ADR.
Collapse
Affiliation(s)
- Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Jotam G Pasipanodya
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Paula Bendet
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Thearith Koeuth
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Pooi S Lee
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Scott K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| |
Collapse
|
7
|
Deshpande D, Pasipanodya JG, Mpagama SG, Bendet P, Srivastava S, Koeuth T, Lee PS, Bhavnani SM, Ambrose PG, Thwaites G, Heysell SK, Gumbo T. Levofloxacin Pharmacokinetics/Pharmacodynamics, Dosing, Susceptibility Breakpoints, and Artificial Intelligence in the Treatment of Multidrug-resistant Tuberculosis. Clin Infect Dis 2018; 67:S293-S302. [PMID: 30496461 PMCID: PMC6260169 DOI: 10.1093/cid/ciy611] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [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: 01/26/2023] Open
Abstract
Background Levofloxacin is used for the treatment of multidrug-resistant tuberculosis; however the optimal dose is unknown. Methods We used the hollow fiber system model of tuberculosis (HFS-TB) to identify 0-24 hour area under the concentration-time curve (AUC0-24) to minimum inhibitory concentration (MIC) ratios associated with maximal microbial kill and suppression of acquired drug resistance (ADR) of Mycobacterium tuberculosis (Mtb). Levofloxacin-resistant isolates underwent whole-genome sequencing. Ten thousands patient Monte Carlo experiments (MCEs) were used to identify doses best able to achieve the HFS-TB-derived target exposures in cavitary tuberculosis and tuberculous meningitis. Next, we used an ensemble of artificial intelligence (AI) algorithms to identify the most important predictors of sputum conversion, ADR, and death in Tanzanian patients with pulmonary multidrug-resistant tuberculosis treated with a levofloxacin-containing regimen. We also performed probit regression to identify optimal levofloxacin doses in Vietnamese tuberculous meningitis patients. Results In the HFS-TB, the AUC0-24/MIC associated with maximal Mtb kill was 146, while that associated with suppression of resistance was 360. The most common gyrA mutations in resistant Mtb were Asp94Gly, Asp94Asn, and Asp94Tyr. The minimum dose to achieve target exposures in MCEs was 1500 mg/day. AI algorithms identified an AUC0-24/MIC of 160 as predictive of microbiologic cure, followed by levofloxacin 2-hour peak concentration and body weight. Probit regression identified an optimal dose of 25 mg/kg as associated with >90% favorable response in adults with pulmonary tuberculosis. Conclusions The levofloxacin dose of 25 mg/kg or 1500 mg/day was adequate for replacement of high-dose moxifloxacin in treatment of multidrug-resistant tuberculosis.
Collapse
Affiliation(s)
- Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Jotam G Pasipanodya
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | - Paula Bendet
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Thearith Koeuth
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Pooi S Lee
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | - Paul G Ambrose
- Institute for Clinical Pharmacodynamics, Schenectady, New York
| | - Guy Thwaites
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, Churchill Hospital, Oxford, United Kingdom
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Scott K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| |
Collapse
|
8
|
Deshpande D, Srivastava S, Chapagain M, Magombedze G, Martin KR, Cirrincione KN, Lee PS, Koeuth T, Dheda K, Gumbo T. Ceftazidime-avibactam has potent sterilizing activity against highly drug-resistant tuberculosis. Sci Adv 2017; 3:e1701102. [PMID: 28875168 PMCID: PMC5576880 DOI: 10.1126/sciadv.1701102] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
There are currently many patients with multidrug-resistant and extensively drug-resistant tuberculosis. Ongoing transmission of the highly drug-resistant strains and high mortality despite treatment remain problematic. The current strategy of drug discovery and development takes up to a decade to bring a new drug to clinical use. We embarked on a strategy to screen all antibiotics in current use and examined them for use in tuberculosis. We found that ceftazidime-avibactam, which is already used in the clinic for multidrug-resistant Gram-negative bacillary infections, markedly killed rapidly growing, intracellular, and semidormant Mycobacterium tuberculosis in the hollow fiber system model. Moreover, multidrug-resistant and extensively drug-resistant clinical isolates demonstrated good ceftazidime-avibactam susceptibility profiles and were inhibited by clinically achievable concentrations. Resistance arose because of mutations in the transpeptidase domain of the penicillin-binding protein PonA1, suggesting that the drug kills M. tuberculosis bacilli via interference with cell wall remodeling. We identified concentrations (exposure targets) for optimal effect in tuberculosis, which we used with susceptibility results in computer-aided clinical trial simulations to identify doses for immediate clinical use as salvage therapy for adults and young children. Moreover, this work provides a roadmap for efficient and timely evaluation of antibiotics and optimization of clinically relevant dosing regimens.
Collapse
Affiliation(s)
- Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | - Moti Chapagain
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | - Gesham Magombedze
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | - Katherine R. Martin
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | - Kayle N. Cirrincione
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | - Pooi S. Lee
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | - Thearith Koeuth
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology and University of Cape Town (UCT) Lung Institute, Department of Medicine, UCT, Observatory, 7925, Cape Town, South Africa
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
- Lung Infection and Immunity Unit, Division of Pulmonology and University of Cape Town (UCT) Lung Institute, Department of Medicine, UCT, Observatory, 7925, Cape Town, South Africa
| |
Collapse
|
9
|
Katerndahl C, Willette M, Heltemes L, Ramsey L, Koeuth T, Gillespie E, Farrar M. STAT5 antagonizes the pre-BCR-dependent NFκB and FOXO tumor suppressor pathways in acute lymphoblastic leukemia (HEM2P.261). The Journal of Immunology 2014. [DOI: 10.4049/jimmunol.192.supp.50.6] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Mice expressing a constitutively active form of STAT5b (Stat5b-CA mice) develop pre-B leukemia with low frequency (~1-2%). Microarray analysis of these leukemias shows decreased expression of genes involved in pre-BCR signaling. Stat5b-CA mice crossed to mice with defects in a coherent signaling pathway downstream of the pre-BCR involving BLNK, BTK, or PKCβ developed pre-B leukemia in > 75% of progeny. These leukemias exhibited reduced expression of a subset of NFκB target genes, which was important for transformation as Stat5b-CA x Nfkb1-/- mice also developed pre-B leukemia. Our results point to an unexpected role for NFκB1 as a tumor suppressor in pre-B cells. Microarrary analysis revealed that STAT5 activation resulted in reduced expression of several NFκB and FOXO target genes, thereby antagonizing these tumor suppressor pathways. To examine this regulation in further detail, we performed ChIP-seq analysis, which showed that STAT5 binds 38% of NFκB target genes that are expressed in pre-B cells. We also observed binding of STAT5 to several FOXO targets including: Foxo1, Cdkn1a, Cdkn2d, Blnk, Vegfa, Cxcr4, Bim, and Dgka. We have validated STAT5 binding to the FOXO targets Foxo1 and Cdkn2d and the NFκB targets Nfkb1, Rel, Irf4, Irf8, Ikzf1, and Ikzf3 by ChIP-qPCR. Our findings demonstrate that STAT5 activation antagonizes the pre-BCR-dependent NFκB and FOXO tumor suppressor pathways that limit pre-B cell proliferation and promote pre-B cell differentiation.
Collapse
Affiliation(s)
- Casey Katerndahl
- 1Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Mark Willette
- 1Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Lynn Heltemes
- 1Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Laura Ramsey
- 1Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Thearith Koeuth
- 2Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Emily Gillespie
- 2Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Michael Farrar
- 1Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| |
Collapse
|
10
|
Katerndahl C, Heltemes-Harris L, Willette M, Ramsey L, Koeuth T, Baechler E, Farrar M. A pre-BCR/NFκB pathway suppresses STAT5-dependent pre-B cell leukemia (P4408). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.52.24] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Mice expressing a constitutively active form of STAT5b (called Stat5b-CA mice) develop pre-B leukemia with low frequency (~1-2%). Microarray analysis of these leukemias shows decreased expression of genes involved in pre-BCR signaling. Stat5b-CA mice crossed to mice with defects in a coherent signaling pathway downstream of the pre-BCR involving BLNK, BTK, or PKCβ developed pre-B leukemia in > 75% of progeny. These leukemias exhibited reduced expression of a subset of NFκB target genes, which was important for transformation as Stat5b-CA x Nfkb1-/- mice also developed pre-B leukemia. Our results point to an unexpected role for NFκB1 as a tumor suppressor in pre-B cells. We found that STAT5 cooperates with defects in this pre-BCR-dependent pathway to repress expression of the potential tumor suppressor genes Foxo1, Foxo3a, Ikzf1, and Ikzf3. Our findings demonstrate that STAT5 activation antagonizes a pre-BCR-dependent pathway that limits pre-B cell proliferation, promotes pre-B cell differentiation, and inhibits pre-B cell transformation.
Collapse
Affiliation(s)
- Casey Katerndahl
- 1Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | - Mark Willette
- 1Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Laura Ramsey
- 1Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | | | - Michael Farrar
- 1Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| |
Collapse
|
11
|
Bilgic H, Koeuth T, Wilson J, Petri M, Baechler Gillespie E. Serum chemokine levels predict flares of disease activity in two independent systemic lupus erythematosus cohorts. Arthritis Res Ther 2012. [PMCID: PMC3467487 DOI: 10.1186/ar3944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
12
|
Katerndahl C, Willette M, Heltemes-Harris L, Ramsey L, Koeuth T, Baechler E, Farrar M. A Pre-BCR/NFκB Pathways Suppresses STAT5-dependent Pre-B Cell Leukemia (111.18). The Journal of Immunology 2012. [DOI: 10.4049/jimmunol.188.supp.111.18] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Mice expressing a constitutively active form of STAT5b (called Stat5b-CA mice) develop pre-B leukemia with low frequency (~1-2%). Microarray analysis of these leukemias shows decreased expression of genes involved in pre-BCR signaling. Stat5b-CA mice crossed to mice with defects in a coherent signaling pathway downstream of the pre-BCR involving BLNK, BTK, or PKCβ developed pre-B leukemia in > 75% of progeny. These leukemias exhibited reduced expression of a subset of NFκB target genes, which was important for transformation as Stat5b-CA x Nfkb1-/- mice also developed pre-B leukemia. Our results point to an unexpected role for NFκB1 as a tumor suppressor in pre-B cells. We found that STAT5 cooperates with defects in this pre-BCR-dependent pathway to repress expression of the potential tumor suppressor genes Foxo1, Foxo3a, Ikzf1, and Ikzf3. Our findings demonstrate that STAT5 activation antagonizes a pre-BCR-dependent pathway that limits pre-B cell proliferation, promote pre-B cell differentiation, and inhibit pre-B cell transformation.
Collapse
Affiliation(s)
- Casey Katerndahl
- 1Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Mark Willette
- 1Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Lynn Heltemes-Harris
- 1Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Laura Ramsey
- 1Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Thearith Koeuth
- 2Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Emily Baechler
- 2Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Michael Farrar
- 1Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN
| |
Collapse
|
13
|
Heltemes-Harris LM, Willette MJ, Ramsey LB, Qiu YH, Neeley ES, Zhang N, Thomas DA, Koeuth T, Baechler EC, Kornblau SM, Farrar MA. Ebf1or Pax5haploinsufficiency synergizes with STAT5 activation to initiate acute lymphoblastic leukemia. J Biophys Biochem Cytol 2011. [DOI: 10.1083/jcb1935oia13] [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: 11/22/2022] Open
|
14
|
Heltemes-Harris LM, Willette MJL, Ramsey LB, Qiu YH, Neeley ES, Zhang N, Thomas DA, Koeuth T, Baechler EC, Kornblau SM, Farrar MA. Ebf1 or Pax5 haploinsufficiency synergizes with STAT5 activation to initiate acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2011; 208:1135-49. [PMID: 21606506 PMCID: PMC3173246 DOI: 10.1084/jem.20101947] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
As STAT5 is critical for the differentiation, proliferation, and survival of progenitor B cells, this transcription factor may play a role in acute lymphoblastic leukemia (ALL). Here, we show increased expression of activated signal transducer and activator of transcription 5 (STAT5), which is correlated with poor prognosis, in ALL patient cells. Mutations in EBF1 and PAX5, genes critical for B cell development have also been identified in human ALL. To determine whether mutations in Ebf1 or Pax5 synergize with STAT5 activation to induce ALL, we crossed mice expressing a constitutively active form of STAT5 (Stat5b-CA) with mice heterozygous for Ebf1 or Pax5. Haploinsufficiency of either Pax5 or Ebf1 synergized with Stat5b-CA to rapidly induce ALL in 100% of the mice. The leukemic cells displayed reduced expression of both Pax5 and Ebf1, but this had little effect on most EBF1 or PAX5 target genes. Only a subset of target genes was deregulated; this subset included a large percentage of potential tumor suppressor genes and oncogenes. Further, most of these genes appear to be jointly regulated by both EBF1 and PAX5. Our findings suggest a model whereby small perturbations in a self-reinforcing network of transcription factors critical for B cell development, specifically PAX5 and EBF1, cooperate with STAT5 activation to initiate ALL.
Collapse
Affiliation(s)
- Lynn M Heltemes-Harris
- Department of Laboratory Medicine and Pathology, The Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Bauer JW, Petri M, Batliwalla FM, Koeuth T, Wilson J, Slattery C, Panoskaltsis-Mortari A, Gregersen PK, Behrens TW, Baechler EC. Interferon-regulated chemokines as biomarkers of systemic lupus erythematosus disease activity: a validation study. ACTA ACUST UNITED AC 2009; 60:3098-107. [PMID: 19790071 DOI: 10.1002/art.24803] [Citation(s) in RCA: 226] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by unpredictable flares of disease activity and irreversible damage to multiple organ systems. An earlier study showed that SLE patients carrying an interferon (IFN) gene expression signature in blood have elevated serum levels of IFN-regulated chemokines. These chemokines were associated with more-severe and active disease and showed promise as SLE disease activity biomarkers. This study was designed to validate IFN-regulated chemokines as biomarkers of SLE disease activity in 267 SLE patients followed up longitudinally. METHODS To validate the potential utility of serum chemokine levels as biomarkers of disease activity, we measured serum levels of CXCL10 (IFNgamma-inducible 10-kd protein), CCL2 (monocyte chemotactic protein 1), and CCL19 (macrophage inflammatory protein 3beta) in an independent cohort of 267 SLE patients followed up longitudinally over 1 year (1,166 total clinic visits). RESULTS Serum chemokine levels correlated with lupus activity at the current visit (P = 2 x 10(-10)), rising at the time of SLE flare (P = 2 x 10(-3)) and decreasing as disease remitted (P = 1 x 10(-3)); they also performed better than the currently available laboratory tests. Chemokine levels measured at a single baseline visit in patients with a Systemic Lupus Erythematosus Disease Activity Index of < or =4 were predictive of lupus flare over the ensuing year (P = 1 x 10(-4)). CONCLUSION Monitoring serum chemokine levels in SLE may improve the assessment of current disease activity, the prediction of future disease flares, and the overall clinical decision-making.
Collapse
|
16
|
Bilgic H, Ytterberg SR, Amin S, McNallan KT, Wilson JC, Koeuth T, Ellingson S, Newman B, Bauer JW, Peterson EJ, Baechler EC, Reed AM. Interleukin-6 and type I interferon-regulated genes and chemokines mark disease activity in dermatomyositis. ACTA ACUST UNITED AC 2009; 60:3436-46. [DOI: 10.1002/art.24936] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
17
|
Graham RR, Kyogoku C, Sigurdsson S, Vlasova IA, Davies LRL, Baechler EC, Plenge RM, Koeuth T, Ortmann WA, Hom G, Bauer JW, Gillett C, Burtt N, Cunninghame Graham DS, Onofrio R, Petri M, Gunnarsson I, Svenungsson E, Rönnblom L, Nordmark G, Gregersen PK, Moser K, Gaffney PM, Criswell LA, Vyse TJ, Syvänen AC, Bohjanen PR, Daly MJ, Behrens TW, Altshuler D. Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc Natl Acad Sci U S A 2007; 104:6758-63. [PMID: 17412832 PMCID: PMC1847749 DOI: 10.1073/pnas.0701266104] [Citation(s) in RCA: 364] [Impact Index Per Article: 21.4] [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: 01/15/2023] Open
Abstract
Systematic genome-wide studies to map genomic regions associated with human diseases are becoming more practical. Increasingly, efforts will be focused on the identification of the specific functional variants responsible for the disease. The challenges of identifying causal variants include the need for complete ascertainment of genetic variants and the need to consider the possibility of multiple causal alleles. We recently reported that risk of systemic lupus erythematosus (SLE) is strongly associated with a common SNP in IFN regulatory factor 5 (IRF5), and that this variant altered spicing in a way that might provide a functional explanation for the reproducible association to SLE risk. Here, by resequencing and genotyping in patients with SLE, we find evidence for three functional alleles of IRF5: the previously described exon 1B splice site variant, a 30-bp in-frame insertion/deletion variant of exon 6 that alters a proline-, glutamic acid-, serine- and threonine-rich domain region, and a variant in a conserved polyA+ signal sequence that alters the length of the 3' UTR and stability of IRF5 mRNAs. Haplotypes of these three variants define at least three distinct levels of risk to SLE. Understanding how combinations of variants influence IRF5 function may offer etiological and therapeutic insights in SLE; more generally, IRF5 and SLE illustrates how multiple common variants of the same gene can together influence risk of common disease.
Collapse
Affiliation(s)
- Robert R. Graham
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Chieko Kyogoku
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Snaevar Sigurdsson
- Molecular Medicine, Department of Medical Sciences, Uppsala University, SE-751 Uppsala, Sweden
| | - Irina A. Vlasova
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Leela R. L. Davies
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Emily C. Baechler
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Robert M. Plenge
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Thearith Koeuth
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Ward A. Ortmann
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Geoffrey Hom
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Jason W. Bauer
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Clarence Gillett
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Noel Burtt
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | | | - Robert Onofrio
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Michelle Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Iva Gunnarsson
- Department of Medicine, Rheumatology Unit, Karolinska Institutet/Karolinska University Hospital, SE-771 Stockholm, Sweden
| | - Elisabet Svenungsson
- Department of Medicine, Rheumatology Unit, Karolinska Institutet/Karolinska University Hospital, SE-771 Stockholm, Sweden
| | - Lars Rönnblom
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, SE-751 Uppsala, Sweden
| | - Gunnel Nordmark
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, SE-751 Uppsala, Sweden
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, NY 11030
| | - Kathy Moser
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Patrick M. Gaffney
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Lindsey A. Criswell
- Department of Medicine, University of California, San Francisco, CA 94143; and
| | - Timothy J. Vyse
- Rheumatology Section, Imperial College, Hammersmith Hospital, London W12 0NN, United Kingdom
| | - Ann-Christine Syvänen
- Molecular Medicine, Department of Medical Sciences, Uppsala University, SE-751 Uppsala, Sweden
| | - Paul R. Bohjanen
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Timothy W. Behrens
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - David Altshuler
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
18
|
Sekine H, Ferreira RC, Pan-Hammarström Q, Graham RR, Ziemba B, de Vries SS, Liu J, Hippen K, Koeuth T, Ortmann W, Iwahori A, Elliott MK, Offer S, Skon C, Du L, Novitzke J, Lee AT, Zhao N, Tompkins JD, Altshuler D, Gregersen PK, Cunningham-Rundles C, Harris RS, Her C, Nelson DL, Hammarström L, Gilkeson GS, Behrens TW. Role for Msh5 in the regulation of Ig class switch recombination. Proc Natl Acad Sci U S A 2007; 104:7193-8. [PMID: 17409188 PMCID: PMC1855370 DOI: 10.1073/pnas.0700815104] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ig class switch recombination (CSR) and somatic hypermutation serve to diversify antibody responses and are orchestrated by the activity of activation-induced cytidine deaminase and many proteins involved in DNA repair and genome surveillance. Msh5, a gene encoded in the central MHC class III region, and its obligate heterodimerization partner Msh4 have a critical role in regulating meiotic homologous recombination and have not been implicated in CSR. Here, we show that MRL/lpr mice carrying a congenic H-2(b/b) MHC interval exhibit several abnormalities regarding CSR, including a profound deficiency of IgG3 in most mice and long microhomologies at Ig switch (S) joints. We found that Msh5 is expressed at low levels on the H-2(b) haplotype and, importantly, a similar long S joint microhomology phenotype was observed in both Msh5 and Msh4-null mice. We also present evidence that genetic variation in MSH5 is associated with IgA deficiency and common variable immune deficiency (CVID) in humans. One of the human MSH5 alleles identified contains two nonsynonymous polymorphisms, and the variant protein encoded by this allele shows impaired binding to MSH4. Similar to the mice, Ig S joints from CVID and IgA deficiency patients carrying disease-associated MSH5 alleles show increased donor/acceptor microhomology, involving pentameric DNA repeat sequences and lower mutation rates than controls. Our findings suggest that Msh4/5 heterodimers contribute to CSR and support a model whereby Msh4/5 promotes the resolution of DNA breaks with low or no terminal microhomology by a classical nonhomologous end-joining mechanism while possibly suppressing an alternative microhomology-mediated pathway.
Collapse
Affiliation(s)
| | | | | | - Robert R. Graham
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Beth Ziemba
- University of Minnesota Medical School, Minneapolis, MN 55455
| | | | - Jiabin Liu
- University of Minnesota Medical School, Minneapolis, MN 55455
| | - Keli Hippen
- University of Minnesota Medical School, Minneapolis, MN 55455
| | - Thearith Koeuth
- University of Minnesota Medical School, Minneapolis, MN 55455
| | - Ward Ortmann
- University of Minnesota Medical School, Minneapolis, MN 55455
| | - Akiko Iwahori
- Medical University of South Carolina, Charleston, SC 29425
| | | | - Steven Offer
- University of Minnesota Medical School, Minneapolis, MN 55455
| | - Cara Skon
- University of Minnesota Medical School, Minneapolis, MN 55455
| | - Likun Du
- Karolinska University Hospital, SE-141 86 Huddinge, Sweden
| | - Jill Novitzke
- University of Minnesota Medical School, Minneapolis, MN 55455
| | - Annette T. Lee
- Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Nianxi Zhao
- Washington State University, Pullman, WA 99164
| | | | - David Altshuler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
| | | | | | | | | | | | | | | | - Timothy W. Behrens
- University of Minnesota Medical School, Minneapolis, MN 55455
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
19
|
Graham RR, Kozyrev SV, Baechler EC, Reddy MVPL, Plenge RM, Bauer JW, Ortmann WA, Koeuth T, González Escribano MF, Pons-Estel B, Petri M, Daly M, Gregersen PK, Martín J, Altshuler D, Behrens TW, Alarcón-Riquelme ME. A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus. Nat Genet 2006; 38:550-5. [PMID: 16642019 DOI: 10.1038/ng1782] [Citation(s) in RCA: 493] [Impact Index Per Article: 27.4] [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: 12/06/2005] [Accepted: 03/14/2006] [Indexed: 01/15/2023]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by activation of the type I interferon (IFN) pathway. Here we convincingly replicate association of the IFN regulatory factor 5 (IRF5) rs2004640 T allele with SLE in four independent case-control cohorts (P = 4.4 x 10(-16)) and by family-based transmission disequilibrium test analysis (P = 0.0006). The rs2004640 T allele creates a 5' donor splice site in an alternate exon 1 of IRF5, allowing expression of several unique IRF5 isoforms. We also identify an independent cis-acting variant associated with elevated expression of IRF5 and linked to the exon 1B splice site. Haplotypes carrying the variant associated with elevated expression and lacking the exon 1B donor site do not confer risk of SLE. Thus, a common IRF5 haplotype driving elevated expression of multiple unique isoforms of IRF5 is an important genetic risk factor for SLE, establishing a causal role for type I IFN pathway genes in human autoimmunity.
Collapse
Affiliation(s)
- Robert R Graham
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Britton RA, Chen SM, Wallis D, Koeuth T, Powell BS, Shaffer LG, Largaespada D, Jenkins NA, Copeland NG, Court DL, Lupski JR. Isolation and preliminary characterization of the human and mouse homologues of the bacterial cell cycle gene era. Genomics 2000; 67:78-82. [PMID: 10945472 DOI: 10.1006/geno.2000.6243] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Era is an essential GTPase that is required for proper cell cycle progression and cell division in Escherichia coli and is found in nearly all bacteria sequenced to date. To determine whether Era is also present in eukaryotic organisms, we searched the dbEST database and found EST clones coding for proteins that were similar to Era. Full sequencing of these ESTs from human and mouse identified a conserved homologue, ERAL1 (Era-like 1). ERAL1 maps to 17q11.2 in human and is located in the syntenic region of mouse chromosome 11. ERAL1 may be an attractive candidate for a tumor suppressor gene since ERAL1 is located in a chromosomal region where loss of heterozygosity is often associated with various types of cancer.
Collapse
Affiliation(s)
- R A Britton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Potocki L, Chen KS, Koeuth T, Killian J, Iannaccone ST, Shapira SK, Kashork CD, Spikes AS, Shaffer LG, Lupski JR. DNA rearrangements on both homologues of chromosome 17 in a mildly delayed individual with a family history of autosomal dominant carpal tunnel syndrome. Am J Hum Genet 1999; 64:471-8. [PMID: 9973284 PMCID: PMC1377756 DOI: 10.1086/302240] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [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: 11/03/2022] Open
Abstract
Disorders known to be caused by molecular and cytogenetic abnormalities of the proximal short arm of chromosome 17 include Charcot-Marie-Tooth disease type 1A (CMT1A), hereditary neuropathy with liability to pressure palsies (HNPP), Smith-Magenis syndrome (SMS), and mental retardation and congenital anomalies associated with partial duplication of 17p. We identified a patient with multifocal mononeuropathies and mild distal neuropathy, growth hormone deficiency, and mild mental retardation who was found to have a duplication of the SMS region of 17p11.2 and a deletion of the peripheral myelin protein 22 (PMP22) gene within 17p12 on the homologous chromosome. Further molecular analyses reveal that the dup(17)(p11.2p11.2) is a de novo event but that the PMP22 deletion is familial. The family members with deletions of PMP22 have abnormalities indicative of carpal tunnel syndrome, documented by electrophysiological studies prior to molecular analysis. The chromosomal duplication was shown by interphase FISH analysis to be a tandem duplication. These data indicate that familial entrapment neuropathies, such as carpal tunnel syndrome and focal ulnar neuropathy syndrome, can occur because of deletions of the PMP22 gene. The co-occurrence of the 17p11.2 duplication and the PMP22 deletion in this patient likely reflects the relatively high frequency at which these abnormalities arise and the underlying molecular characteristics of the genome in this region.
Collapse
Affiliation(s)
- L Potocki
- Departments of Molecular and Human Genetics,Baylor College of Medicine,Houston, TX 77030, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Reiter L, Murakami T, Koeuth T, Pentao L, Muzny D, Gibbs R, Lupski J. Correction: A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nat Genet 1998. [DOI: 10.1038/998] [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: 11/09/2022]
|
23
|
Abstract
The presence of a Salmonella serotype Enteritidis repeat element (SERE) located within the upstream regulatory region of the sefABCD operon encoding fimbrial proteins is reported. DNA dot-blot hybridisation analyses and computerised searches of genetic databases indicate that SERE is well conserved and widely distributed throughout the bacterial and archaeal kingdoms. A SERE-based polymerase chain reaction (SERE-PCR) assay was developed to fingerprint 54 isolates of Enteritidis representing nine distinct phage types and 54 isolates of other Salmonella serotypes. SERE-PCR identified five distinct fingerprint profiles among the 54 Enteritidis isolates; no correlation between phage types and SERE-PCR fingerprint patterns was noticed. SERE-PCR was reproducible, rapid and easy to perform. The results of this investigation suggest that the limited heterogeneity of SERE-PCR fingerprint patterns can be utilised to develop serotype- and serogroup-specific fingerprint patterns for isolates of Enteritidis.
Collapse
Affiliation(s)
- G Rajashekara
- Department of Veterinary PathoBiology, University of Minnesota, St Paul 55108, USA
| | | | | | | | | | | | | |
Collapse
|
24
|
Chen KS, Manian P, Koeuth T, Potocki L, Zhao Q, Chinault AC, Lee CC, Lupski JR. Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nat Genet 1997; 17:154-63. [PMID: 9326934 DOI: 10.1038/ng1097-154] [Citation(s) in RCA: 296] [Impact Index Per Article: 11.0] [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: 02/05/2023]
Abstract
Smith-Magenis syndrome (SMS), caused by del(17)p11.2, represents one of the most frequently observed human microdeletion syndromes. We have identified three copies of a low-copy-number repeat (SMS-REPs) located within and flanking the SMS common deletion region and show that SMS-REP represents a repeated gene cluster. We have isolated a corresponding cDNA clone that identifies a novel junction fragment from 29 unrelated SMS patients and a different-sized junction fragment from a patient with dup(17)p11.2. Our results suggest that homologous recombination of a flanking repeat gene cluster is a mechanism for this common microdeletion syndrome.
Collapse
Affiliation(s)
- K S Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Reiter LT, Murakami T, Koeuth T, Gibbs RA, Lupski JR. The human COX10 gene is disrupted during homologous recombination between the 24 kb proximal and distal CMT1A-REPs. Hum Mol Genet 1997; 6:1595-603. [PMID: 9285799 DOI: 10.1093/hmg/6.9.1595] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.4] [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: 02/05/2023] Open
Abstract
The CMT1A-REPs are two large directly repeating DNA sequences located on chromosome 17p11.2-p12 flanking the region duplicated in patients with Charcot-Marie-Tooth disease type 1A (CMT1A) and deleted in patients with hereditary neuropathy with liability to pressure palsies (HNPP). We have sequenced two cosmids, c74F4 and c15H12, which contain the entire proximal and distal CMT1A-REPs and determined that these repeats are approximately 99% identical across a 24,011 bp region. In addition, both contain an exon of the human heme A:farnesyltransferase gene (COX10). Hybridization studies revealed that COX10 spans the distal CMT1A-REP, while the proximal CMT1A-REP contains an isolated COX10 'pseudo-exon'. There is also a COX10 hybridization signal on chromosome 10 which appears to represent a processed pseudogene. We propose that the distal CMT1A-REP represents the progenitor copy of COX10 exon VI which was duplicated with surrounding intronic sequences during mammalian genome evolution and that the HNPP deletion results in a COX10 null allele.
Collapse
Affiliation(s)
- L T Reiter
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | |
Collapse
|
26
|
Timmerman V, Rautenstrauss B, Reiter LT, Koeuth T, Löfgren A, Liehr T, Nelis E, Bathke KD, De Jonghe P, Grehl H, Martin JJ, Lupski JR, Van Broeckhoven C. Detection of the CMT1A/HNPP recombination hotspot in unrelated patients of European descent. J Med Genet 1997; 34:43-9. [PMID: 9032649 PMCID: PMC1050846 DOI: 10.1136/jmg.34.1.43] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Charcot-Marie-Tooth type 1 disease (CMT1) and hereditary neuropathy with liability to pressure palsies (HNPP) are common inherited disorders of the peripheral nervous system. The majority of CMT1 patients have a 1.5Mb tandem duplication (CMT1A) in chromosome 17p11.2 while most HNPP patients have a deletion of the same 1.5 Mb region. The CMT1A duplication and HNPP deletion are the reciprocal products of an unequal crossing over event between misaligned flanking CMT1A-REP elements. We analysed 162 unrelated CMT1A duplication patients and HNPP deletion patients from 11 different countries for the presence of a recombination hotspot in the CMT1A-REP sequences. A hotspot for unequal crossing over between the misaligned flanking CMT1A-REP elements was observed through the detection of novel junction fragments in 76.9% of 130 unrelated CMT1A patients and in 71.9% of 32 unrelated HNPP patients. This recombination hotspot was also detected in eight out of 10 de novo CMT1A duplication and in two de novo HNPP deletion patients. These data indicate that the hotspot of unequal crossing over occurs in several populations independently of ethnic background and is directly involved in the pathogenesis of CMT1A and HNPP. We conclude that the detection of junction fragments from the CMT1A-REP element on Southern blot analysis is a simple and reliable DNA diagnostic tool for the identification of the CMT1A duplication and HNPP deletion in most patients.
Collapse
Affiliation(s)
- V Timmerman
- Flanders Interuniversity Institute of Biotechnology (VIB), Born-Bunge Foundation (BBS), University of Antwerp (UIA), Department of Biochemistry, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Woods CR, Koeuth T, Estabrook MM, Lupski JR. Rapid determination of outbreak-related strains of Neisseria meningitidis by repetitive element-based polymerase chain reaction genotyping. J Infect Dis 1996; 174:760-7. [PMID: 8843214 DOI: 10.1093/infdis/174.4.760] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Outbreaks of invasive disease caused by Neisseria meningitidis have increased in the United States in the 1990s. Repetitive element-based polymerase chain reaction (rep-PCR), a recently developed genotyping method, was used to evaluate a group of 8 outbreak-related and 35 other meningococcal isolates previously typed by multilocus enzyme electrophoresis (MLEE). All were serogroup B or C. Sets of genotypes were generated using primers based on either of two different repetitive sequences. Genotype sets were analyzed in a blinded fashion. Each set correctly identified outbreak-related isolates. Among the other 35 isolates, rep-PCR delineated 14 and 13 strains, respectively, in the two sets of genotypes. Seventeen electrophoretic types had been delineated by MLEE. Rep-PCR holds promise as a rapid, genome-based typing method for delineation of apparent outbreaks of meningococcal disease.
Collapse
Affiliation(s)
- C R Woods
- Department of Pediatrics, Bowman Gray School of Medicine, Wake Forest University, Winston-Salem, North Carolina 27157, USA
| | | | | | | |
Collapse
|
28
|
Allerberger F, Koeuth T, Lass-FLörl C, Dierich MP, Putensen C, Scmutzhard E, Mohsenipour I, Grundmann H, Hartung D, Bauernfeind A, Eberlein E, Lupski JR. Epidemiology of infections due to multiresistant Enterobacter aerogenes in a university hospital. Eur J Clin Microbiol Infect Dis 1996; 15:517-21. [PMID: 8839650 DOI: 10.1007/bf01691323] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
29
|
Reiter LT, Murakami T, Koeuth T, Pentao L, Muzny DM, Gibbs RA, Lupski JR. A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nat Genet 1996; 12:288-97. [PMID: 8589720 DOI: 10.1038/ng0396-288] [Citation(s) in RCA: 230] [Impact Index Per Article: 8.2] [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: 01/31/2023]
Abstract
The Charcot-Marie Tooth disease type 1A (CMT1A) duplication and hereditary neuropathy with liability to pressure palsies (HNPP) deletion are reciprocal products of an unequal crossing-over event between misaligned flanking CMT1A-REP repeats. The molecular aetiology of this apparently homologous recombination event was examined by sequencing the crossover region. Through the detection of novel junction fragments from the recombinant CMT1A-REPs in both CMT1A and HNPP patients, a 1.7-kb recombination hotspot within the approximately 30-kb CMT1A-REPs was identified. This hotspot is 98% identical between CMT1A-REPs indicating that sequence identity is not likely the sole factor involved in promoting crossover events. Sequence analysis revealed a mariner transposon-like element (MITE) near the hotspot which we hypothesize could mediate strand exchange events via cleavage by a transposase at or near the 3' end of the element.
Collapse
Affiliation(s)
- L T Reiter
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Koeuth T, Versalovic J, Lupski JR. Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria. Genome Res 1995; 5:408-18. [PMID: 8750201 DOI: 10.1101/gr.5.4.408] [Citation(s) in RCA: 188] [Impact Index Per Article: 6.5] [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: 02/02/2023]
Abstract
Evolutionary conservation of an interspersed repetitive DNA sequence, BOX, from Streptococcus pneumoniae was investigated to explore the mosaic nature of these elements. BOX elements consist of various combinations of three subunits, boxA, boxB, and boxC. Eight oligonucleotide probes were designed based on consensus DNA sequences of boxA, boxB, and boxC subunits. DNA hybridization studies and PCR using these probes/primers demonstrate that oligonucleotide sequences within the boxA subunit appear to be conserved among diverse bacterial species. The boxB and boxC subunits show only limited, if any, sequence conservation in bacteria other than S. pneumoniae. Intact BOX elements with boxA, boxB, and boxC subunits were only present in high copy number in pneumococcal strains. This pattern of differential conservation lends support to the modular nature of BOX repetitive elements in that boxA-like subsequences are effectively independent of boxB-like or boxC-like subunits in bacteria other than S. pneumoniae. Furthermore, dendrograms derived from repetitive sequence-based PCR (rep-PCR) fingerprints of S. pneumoniae isolates using the BOXA1R primer yielded clustering patterns that were similar to those obtained previously by other methods, suggesting that these repetitive sequence-based DNA fingerprints represent intrinsic properties of an S. pneumoniae strain's genome. Our results indicate widespread conservation of boxA-like subsequences in the bacterial kingdom, lend support to the mosaic nature of BOX in S. pneumoniae, and demonstrate the utility of boxA-based primers for rep-PCR fingerprinting of many microorganisms.
Collapse
Affiliation(s)
- T Koeuth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | |
Collapse
|
31
|
Harvey BS, Koeuth T, Versalovic J, Woods CR, Lupski JR. Vertical transmission of Citrobacter diversus documented by DNA fingerprinting. Infect Control Hosp Epidemiol 1995; 16:564-9. [PMID: 8568200 DOI: 10.1086/647009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
OBJECTIVE To confirm the vertical transmission of Citrobacter diversus from a mother to her infant and to evaluate the epidemiologic usefulness of a new automated procedure for analysis of polymerase chain reaction (PCR)-generated DNA fingerprints. DESIGN Repetitive element-based PCR (rep-PCR) analysis of C diversus isolates from the blood and amniotic fluid of a mother and the blood of her infant was performed. Unrelated C diversus isolates also were characterized and compared with the isolates from mother and infant. DNA fingerprints were generated by gel electrophoresis of PCR products derived from either unlabeled standard repetitive sequence-based oligonucleotide primers or fluorescent primers. The standard rep-PCR fingerprints were analyzed by visual inspection. The fluorescent primers were used in fluorophore-enhanced rep-PCR (FERP), and the FERP DNA fingerprints were analyzed by an Applied BioSystems (ABI) Model 373A laser scanning unit equipped with Genescan 672 software (Applied Biosystems, Inc, Foster City, CA). SETTING AND PATIENTS A mother and her newborn infant, both with invasive disease due to C diversus, in an urban tertiary-care hospital. RESULTS The DNA fingerprints of the maternal blood, amniotic fluid, and infant blood isolates of C diversus were identical by both visual inspection of ethidium bromide-stained agarose gels and computer-aided analysis of FERP patterns. These strains appeared to differ from all but one control isolate, which had been collected 7 years earlier in the same city in which the infant was born. CONCLUSIONS Vertical transmission of C diversus from mother to infant can occur in utero. Automated analysis of rep-PCR-generated DNA fingerprints derived using fluorescent primers is an objective means for comparing isolates of C diversus and in all likelihood would be useful for other species of bacteria that possess repetitive elements.
Collapse
Affiliation(s)
- B S Harvey
- Department of Pediatrics, University of Texas Health Sciences Center, Houston, USA
| | | | | | | | | |
Collapse
|
32
|
Harvey BS, Koeuth T, Versalovic J, Woods CR, Lupski JR. Vertical Transmission of Citrobacter diversus Documented by DNA Fingerprinting. Infect Control Hosp Epidemiol 1995. [DOI: 10.2307/30141095] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
33
|
Go MF, Chan KY, Versalovic J, Koeuth T, Graham DY, Lupski JR. Cluster analysis of Helicobacter pylori genomic DNA fingerprints suggests gastroduodenal disease-specific associations. Scand J Gastroenterol 1995; 30:640-6. [PMID: 7481525 DOI: 10.3109/00365529509096306] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Helicobacter pylori infection is now accepted as the most common cause of chronic active gastritis and peptic ulcer disease. The etiologies of many infectious diseases have been attributed to specific or clonal strains of bacterial pathogens. Polymerase chain reaction (PCR) amplification of DNA between repetitive DNA sequences, REP elements (REP-PCR), has been utilized to generate DNA fingerprints to examine similarity among strains within a bacterial species. METHODS Genomic DNA from H. pylori isolates obtained from 70 individuals (39 duodenal ulcers and 31 simple gastritis) was PCR-amplified using consensus probes to repetitive DNA elements. The H. pylori DNA fingerprints were analyzed for similarity and correlated with disease presentation using the NTSYS-pc computer program. RESULTS Each H. pylori strain had a distinct DNA fingerprint except for two pairs. Single-colony DNA fingerprints of H. pylori from the same patient were identical, suggesting that each patient harbors a single strain. Computer-assisted cluster analysis of the REP-PCR DNA fingerprints showed two large clusters of isolates, one associated with simple gastritis and the other with duodenal ulcer disease. CONCLUSIONS Cluster analysis of REP-PCR DNA fingerprints of H. pylori strains suggests that duodenal ulcer isolates, as a group, are more similar to one another and different from gastritis isolates. These results suggest that disease-specific strains may exist.
Collapse
Affiliation(s)
- M F Go
- Dept. of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | | | | | | | | | | |
Collapse
|
34
|
Versalovic J, Kapur V, Koeuth T, Mazurek GH, Whittam TS, Musser JM, Lupski JR. DNA fingerprinting of pathogenic bacteria by fluorophore-enhanced repetitive sequence-based polymerase chain reaction. Arch Pathol Lab Med 1995; 119:23-9. [PMID: 7802548] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fluorophore-labeled oligonucleotide primers complementary to defined interspersed repetitive sequences conserved in diverse bacteria were used in the polymerase chain reaction to generate DNA fingerprint patterns from selected pathogenic bacteria. Fluorophore-enhanced, repetitive sequence-based polymerase chain reaction allowed discrimination between unrelated isolates of penicillin-resistant Streptococcus pneumoniae recovered from pediatric patients and Mycobacterium avium cultured from patients with acquired immunodeficiency syndrome. Combinations of oligonucleotide primers labeled with distinct fluorescent dyes enabled simultaneous DNA fingerprinting and Shiga-like toxin gene detection in enterohemorrhagic Escherichia coli isolates. Fluorophore-enhanced, repetitive sequence-based polymerase chain reaction was performed with either purified DNA or intact cells that were lysed during the polymerase chain reaction. Fluorophore-enhanced, repetitive sequence-based polymerase chain reaction successfully combines polymerase chain reaction amplification and fluorescent label detection for DNA fingerprinting of cultured bacterial pathogens.
Collapse
Affiliation(s)
- J Versalovic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | | | | | | | | | | | | |
Collapse
|
35
|
Georghiou PR, Hamill RJ, Wright CE, Versalovic J, Koeuth T, Watson DA, Lupski JR. Molecular epidemiology of infections due to Enterobacter aerogenes: identification of hospital outbreak-associated strains by molecular techniques. Clin Infect Dis 1995; 20:84-94. [PMID: 7727676 DOI: 10.1093/clinids/20.1.84] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Molecular techniques were used to study the epidemiology of infections due to Enterobacter aerogenes in a tertiary-care hospital. Sixty-two clinical isolates were collected from 43 patients over 3 months. Restriction endonuclease analysis (REA) of chromosomal DNA and repetitive-element polymerase chain reaction (rep-PCR) with primers based on repetitive extragenic palindromic (REP) and enterobacterial repetitive intergenic consensus (ERIC) bacterial DNA sequences were used for genomic fingerprinting. REA with HindIII or EcoRI yielded complex banding patterns that differentiated community-acquired from some hospital-acquired organisms. Less complex fingerprints were obtained with rep-PCR, which also distinguished between epidemiologically unrelated strains. More discriminatory DNA fingerprints were provided by rep-PCR when REP primers rather than ERIC primers were used. Two clusters of genomically distinct isolates from patients with recent or current exposure to the hospital environment were identified by REA and rep-PCR. Most isolates within each cluster contained characteristic plasmids, and some isolates contained additional plasmids. These results suggest colonization and infection with genotypically related strains of E. aerogenes in a nosocomial setting. Although REA and plasmid profiling are useful techniques for the epidemiological typing of E. aerogenes, genomic fingerprinting with rep-PCR may offer the advantages of ease, speed, and broad species applicability over existing molecular-typing techniques.
Collapse
Affiliation(s)
- P R Georghiou
- Infectious Disease Section, Veterans Affairs Medical Center, Houston, Texas
| | | | | | | | | | | | | |
Collapse
|
36
|
Woods CR, Versalovic J, Koeuth T, Lupski JR. Whole-cell repetitive element sequence-based polymerase chain reaction allows rapid assessment of clonal relationships of bacterial isolates. J Clin Microbiol 1993; 31:1927-31. [PMID: 8349778 PMCID: PMC265663 DOI: 10.1128/jcm.31.7.1927-1931.1993] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.3] [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: 01/30/2023] Open
Abstract
Repetitive element sequence-based polymerase chain reaction (rep-PCR) enables the generation of DNA fingerprints which discriminate bacterial species and strains. We describe the application of whole-cell methods which allow specimens from broth cultures or colonies from agar plates to be utilized directly in the PCR mixture. The rep-PCR-generated DNA fingerprints obtained with whole-cell samples match results obtained with genomic DNA templates. Examples with different gram-negative bacteria (e.g., Citrobacter diversus, Escherichia coli, and Pseudomonas aeruginosa) and gram-positive bacteria (e.g., Staphylococcus aureus and Streptococcus pneumoniae) are demonstrated. Rapid specimen preparation methods enable rep-PCR-based fingerprinting to be completed in several hours and, therefore, allows the timely analysis of epidemiological relationships.
Collapse
Affiliation(s)
- C R Woods
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030
| | | | | | | |
Collapse
|
37
|
Abstract
The macromolecular synthesis (MMS) operon contains three essential genes (rpsU, dnaG, rpoD) whose products (S21, primase, sigma-70) are necessary for the initiation of protein, DNA, and RNA synthesis respectively. PCR amplifications with primers complementary to conserved regions within these three genes, and subsequent DNA sequencing of rpsU-dnaG PCR products, demonstrate that the three genes appear to be contiguous in 11 different Gram-negative species. Within the Gram-negative enteric bacterial lineage, the S21 amino acid sequence is absolutely conserved in 10 species examined. The putative nuteq antiterminator sequence in rpsU consists of two motifs, boxA and boxB, conserved in primary sequence and secondary structure. The terminator sequence, T1, located between rpsU and dnaG is conserved at 31 positions in nine enterobacterial species, suggesting the importance of primary sequence in addition to secondary structure for transcription termination. The intergenic region between rpsU and dnaG varies in size owing to the presence or absence of the Enterobacterial Repetitive Intergenic Consensus (ERIC) DNA element. The rpoD gene contains rearrangements involving a divergent sequence, although two carboxy-terminal regions which encode functional domains are conserved in primary sequence and spacing. Our data suggest that primary sequence divergence and DNA rearrangements in both coding and non-coding sequences account for the interspecies variation in operon structure. However, MMS operon gene organization and cis-acting regulatory sequences appear to be conserved in diverse bacteria.
Collapse
Affiliation(s)
- J Versalovic
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030
| | | | | | | | | |
Collapse
|
38
|
Versalovic J, Kapur V, Mason EO, Shah U, Koeuth T, Lupski JR, Musser JM. Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones. J Infect Dis 1993; 167:850-6. [PMID: 8450250 DOI: 10.1093/infdis/167.4.850] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A sample of 48 penicillin-resistant Streptococcus pneumoniae (PRSP) strains recovered between January 1989 and May 1991, primarily from infected children in Houston, was characterized by multilocus enzyme electrophoresis and repetitive extragenic palindromic-polymerase chain reaction genomic profiling. A heterogeneous array of 22 clonal genotypes was identified, but 64% of the PRSP strains in the sample were assigned to five clones that are closely similar in overall chromosomal character and express serotype 6 capsule. A close genetic association between these five clones and penicillin-resistant 6B clones recovered in Alaska, Iceland, and Spain was identified by multilocus enzyme electrophoresis. Taken together, the results suggest either that the common resistant 6B clones in Alaska, Iceland, Spain, and Houston have a recent ancestor or that isolates of a certain pneumococcal phylogenetic lineage are more likely to develop penicillin resistance.
Collapse
Affiliation(s)
- J Versalovic
- Dept. of Pathology, Baylor College of Medicine, Houston, TX 77030
| | | | | | | | | | | | | |
Collapse
|
39
|
Woods CR, Versalovic J, Koeuth T, Lupski JR. Analysis of relationships among isolates of Citrobacter diversus by using DNA fingerprints generated by repetitive sequence-based primers in the polymerase chain reaction. J Clin Microbiol 1992; 30:2921-9. [PMID: 1452663 PMCID: PMC270553 DOI: 10.1128/jcm.30.11.2921-2929.1992] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.6] [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: 12/27/2022] Open
Abstract
Oligonucleotide probes which match consensus sequences of the repetitive extragenic palindromic (REP) element hybridize to genomic DNA of diverse bacterial species. Primers based on the REP sequence generate complex band patterns with genomic DNA in the polymerase chain reaction (PCR), a technique named REP-PCR. We used REP-PCR with genomic DNA to fingerprint 47 isolates of Citrobacter diversus. Previously, 37 were assigned electrophoretic types (ETs) by multilocus enzyme electrophoresis and 35 were evaluated by using outer membrane protein profiles. Fingerprints were compared by visual inspection and by similarity coefficients (SimCs) based on the number of common bands versus total bands between two given isolates. DNA fingerprints were highly similar visually for patient pairs and outbreak-related sets. SimCs for these were > or = 0.952. Fingerprints of isolates with different ETs generally were distinctive. Among 21 unrelated isolates representing 15 ETs, only 6 of 210 comparisons had SimCs of > or = 0.952. REP-PCR rapidly generated DNA fingerprints which were highly similar for epidemiologically linked isolates of C. diversus and distinct for previously characterized strains within this species. The ability of this method to discriminate between C. diversus isolates with the same biotype was similar to that of multilocus enzyme electrophoresis and outer membrane protein profiles. REP-PCR may be useful in evaluation of apparent outbreaks of this or other bacterial species which possess these extragenic, repetitive elements.
Collapse
Affiliation(s)
- C R Woods
- C. T. Parker Laboratory, Texas Children's Hospital, Baylor College of Medicine, Houston 77030
| | | | | | | |
Collapse
|
40
|
Versalovic J, Koeuth T, Lupski JR. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 1991; 19:6823-31. [PMID: 1762913 PMCID: PMC329316 DOI: 10.1093/nar/19.24.6823] [Citation(s) in RCA: 2000] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Dispersed repetitive DNA sequences have been described recently in eubacteria. To assess the distribution and evolutionary conservation of two distinct prokaryotic repetitive elements, consensus oligonucleotides were used in polymerase chain reaction [PCR] amplification and slot blot hybridization experiments with genomic DNA from diverse eubacterial species. Oligonucleotides matching Repetitive Extragenic Palindromic [REP] elements and Enterobacterial Repetitive Intergenic Consensus [ERIC] sequences were synthesized and tested as opposing PCR primers in the amplification of eubacterial genomic DNA. REP and ERIC consensus oligonucleotides produced clearly resolvable bands by agarose gel electrophoresis following PCR amplification. These band patterns provided unambiguous DNA fingerprints of different eubacterial species and strains. Both REP and ERIC probes hybridized preferentially to genomic DNA from Gram-negative enteric bacteria and related species. Widespread distribution of these repetitive DNA elements in the genomes of various microorganisms should enable rapid identification of bacterial species and strains, and be useful for the analysis of prokaryotic genomes.
Collapse
Affiliation(s)
- J Versalovic
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, TX 77030
| | | | | |
Collapse
|
41
|
Affiliation(s)
- J Versalovic
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | | | | | | |
Collapse
|
42
|
Lupski JR, Zhang YH, Rieger M, Minter M, Hsu B, Ooi BG, Koeuth T, McCabe ER. Mutational analysis of the Escherichia coli glpFK region with Tn5 mutagenesis and the polymerase chain reaction. J Bacteriol 1990; 172:6129-34. [PMID: 2170343 PMCID: PMC526940 DOI: 10.1128/jb.172.10.6129-6134.1990] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [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: 12/30/2022] Open
Abstract
Transposon Tn5 mutagenesis of the Escherichia coli chromosome was used to isolate 21 independent insertion mutations conferring an altered colony color phenotype on MacConkey-glycerol plates. The polymerase chain reaction was used to map 16 of these Tn5 insertions within the glpFK region at 88 min. The most polar Tn5 insertion was shown by nucleotide sequencing to be in the proposed glpF open reading frame. The data suggest that the glpF and glpK genes are in an operon with a bent DNA segment (BENT-6) involved in transcriptional regulation of this operon.
Collapse
Affiliation(s)
- J R Lupski
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030
| | | | | | | | | | | | | | | |
Collapse
|