Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis

Kedia, Komal; Wendler, Jason P.; Baker, Erin S.; Burnum-Johnson, Kristin E.; Jarsberg, Leah G.; Stratton, Kelly G.; Wright, Aaron T.; Piehowski, Paul D.; Gritsenko, Marina A.; Lewinsohn, David M.; Sigal, George B.; Weiner, Marc H.; Smith, Richard D.; Jacobs, Jon M.; Nahid, Payam

doi:10.1016/j.tube.2018.07.005

Title: Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis

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Abstract

Here, the monitoring of TB treatments in clinical practice and clinical trials relies on traditional sputum-based culture status indicators at specific time points. Accurate, predictive, blood-based protein markers would provide a simpler and more informative view of patient health and response to treatment. We utilized sensitive, high throughput multiplexed ion mobility-mass spectrometry (IM-MS) to characterize the serum proteome of TB patients at the start of and at 8 weeks of rifamycin-based treatment. We sought to identify treatment specific signatures within patients as well as correlate the proteome signatures to various clinical markers of treatment efficacy. Serum samples were collected from 289 subjects enrolled in CDC TB Trials Consortium Study 29 at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Serum proteins were immunoaffinity-depleted of high abundant components, digested to peptides and analyzed for data acquisition utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS). Linear mixed models were utilized to identify serum protein changes in the host response to antibiotic treatment as well as correlations with culture status end points. A total of 10,137 peptides corresponding to 872 proteins were identified, quantified, and used for statistical analysis across the longitudinal patient cohort.more »« less

Authors:

Kedia, Komal; Wendler, Jason P.;

; Burnum-Johnson, Kristin E.;

; Stratton, Kelly G.;

;

; Gritsenko, Marina A.; Lewinsohn, David M.; Sigal, George B.; Weiner, Marc H.; Smith, Richard D.; Jacobs, Jon M.;

Publication Date:: 2018-09-01

Research Org.:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1461904

Alternate Identifier(s):: OSTI ID: 1461645

Report Number(s):: PNNL-SA-126570
Journal ID: ISSN 1472-9792; S1472979218301264; PII: S1472979218301264

Grant/Contract Number:: AC05-76RLO 1830; 1R01AI104589; 200-2009-32597; GM103493; AC05-76RL01830

Resource Type:: Published Article

Journal Name:: Tuberculosis

Additional Journal Information:: Journal Name: Tuberculosis Journal Volume: 112 Journal Issue: C; Journal ID: ISSN 1472-9792

Publisher:: Elsevier

Country of Publication:: Netherlands

Language:: English

Subject:: 60 APPLIED LIFE SCIENCES; Ion mobility spectrometry; Proteomics; Tuberculosis; Antibiotic treatment

Citation Formats


                    Kedia, Komal, Wendler, Jason P., Baker, Erin S., Burnum-Johnson, Kristin E., Jarsberg, Leah G., Stratton, Kelly G., Wright, Aaron T., Piehowski, Paul D., Gritsenko, Marina A., Lewinsohn, David M., Sigal, George B., Weiner, Marc H., Smith, Richard D., Jacobs, Jon M., and Nahid, Payam. Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis.  Netherlands: N. p., 2018. 
Web.  doi:10.1016/j.tube.2018.07.005.

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                    Kedia, Komal, Wendler, Jason P., Baker, Erin S., Burnum-Johnson, Kristin E., Jarsberg, Leah G., Stratton, Kelly G., Wright, Aaron T., Piehowski, Paul D., Gritsenko, Marina A., Lewinsohn, David M., Sigal, George B., Weiner, Marc H., Smith, Richard D., Jacobs, Jon M., & Nahid, Payam. Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis.  Netherlands.  https://doi.org/10.1016/j.tube.2018.07.005

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                    Kedia, Komal, Wendler, Jason P., Baker, Erin S., Burnum-Johnson, Kristin E., Jarsberg, Leah G., Stratton, Kelly G., Wright, Aaron T., Piehowski, Paul D., Gritsenko, Marina A., Lewinsohn, David M., Sigal, George B., Weiner, Marc H., Smith, Richard D., Jacobs, Jon M., and Nahid, Payam. Sat .  
"Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis".  Netherlands.  https://doi.org/10.1016/j.tube.2018.07.005.

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@article{osti_1461904,

  title        = {Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis},

  author       = {Kedia, Komal and Wendler, Jason P. and Baker, Erin S. and Burnum-Johnson, Kristin E. and Jarsberg, Leah G. and Stratton, Kelly G. and Wright, Aaron T. and Piehowski, Paul D. and Gritsenko, Marina A. and Lewinsohn, David M. and Sigal, George B. and Weiner, Marc H. and Smith, Richard D. and Jacobs, Jon M. and Nahid, Payam},

  abstractNote = {Here, the monitoring of TB treatments in clinical practice and clinical trials relies on traditional sputum-based culture status indicators at specific time points. Accurate, predictive, blood-based protein markers would provide a simpler and more informative view of patient health and response to treatment. We utilized sensitive, high throughput multiplexed ion mobility-mass spectrometry (IM-MS) to characterize the serum proteome of TB patients at the start of and at 8 weeks of rifamycin-based treatment. We sought to identify treatment specific signatures within patients as well as correlate the proteome signatures to various clinical markers of treatment efficacy. Serum samples were collected from 289 subjects enrolled in CDC TB Trials Consortium Study 29 at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Serum proteins were immunoaffinity-depleted of high abundant components, digested to peptides and analyzed for data acquisition utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS). Linear mixed models were utilized to identify serum protein changes in the host response to antibiotic treatment as well as correlations with culture status end points. A total of 10,137 peptides corresponding to 872 proteins were identified, quantified, and used for statistical analysis across the longitudinal patient cohort. In response to TB treatment, 244 proteins were significantly altered. Pathway/network comparisons helped visualize the interconnected proteins, identifying up regulated (lipid transport, coagulation cascade, endopeptidase activity) and down regulated (acute phase) processes and pathways in addition to other cross regulated networks (inflammation, cell adhesion, extracellular matrix). Detection of possible lung injury serum proteins such as HPSE, significantly downregulated upon treatment. Analyses of microbiologic data over time identified a core set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2) which change in response to treatment and also strongly correlate with culture status. A similar set of proteins at baseline were found to be predictive of week 6 and 8 culture status.},

  doi          = {10.1016/j.tube.2018.07.005},

  journal      = {Tuberculosis},

  number       = C,

  volume       = 112,

  place        = {Netherlands},

  year         = {2018},

  month        = {9}

}

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