Discovery of Potential Plasma Biomarkers for Tuberculosis in HIV-Infected Patients by Data-Independent Acquisition-Based Quantitative Proteomics

References

• Corbett EL, Watt CJ, Walker N, et al. The growing burden of tuberculosis: global trends and interactions with the HIV epidemic. Arch Intern Med. 2003;163(9):1009–1021. doi:10.1001/archinte.163.9.100912742798
   PubMed Web of Science ®Google Scholar
• Ai JW, Ruan QL, Liu QH, Zhang WH. Updates on the risk factors for latent tuberculosis reactivation and their managements. Emerg Microbes Infect. 2016;5:e10. doi:10.1038/emi.2016.1026839146
   PubMed Web of Science ®Google Scholar
• World Health Organization. Global tuberculosis report. 10, 2019 Available from: https://apps.who.int/iris/bitstream/handle/10665/329368/9789241565714-eng.pdf. Accessed 1212, 2019.
   Google Scholar
• Diedrich CR, Flynn JL. HIV-1/mycobacterium tuberculosis coinfection immunology: how does HIV-1 exacerbate tuberculosis? Infect Immun. 2011;79(4):1407–1417. doi:10.1128/IAI.01126-1021245275
   PubMed Web of Science ®Google Scholar
• Schutz C, Meintjes G, Almajid F, Wilkinson RJ, Pozniak A. Clinical management of tuberculosis and HIV-1 co-infection. Eur Respir J. 2010;36(6):1460–1481. doi:10.1183/09031936.0011021020947678
   PubMed Web of Science ®Google Scholar
• Elliott AM, Namaambo K, Allen BW, et al. Negative sputum smear results in HIV-positive patients with pulmonary tuberculosis in Lusaka, Zambia. Tuber Lung Dis. 1993;74(3):191–194. doi:10.1016/0962-8479(93)90010-U8369514
   PubMedGoogle Scholar
• Lawson L, Yassin MA, Ramsay A, Emenyonu NE, Squire SB, Cuevas LE. Comparison of scanty AFB smears against culture in an area with high HIV prevalence. Int J Tuberc Lung Dis. 2005;9(8):933–935.16104643
   PubMed Web of Science ®Google Scholar
• Hathout Y, Brody E, Clemens PR, et al. Large-scale serum protein biomarker discovery in Duchenne muscular dystrophy. Proc Natl Acad Sci U S A. 2015;112(23):7153–7158. doi:10.1073/pnas.150771911226039989
   PubMed Web of Science ®Google Scholar
• Duangkumpha K, Stoll T, Phetcharaburanin J, et al. Discovery and qualification of serum protein biomarker candidates for cholangiocarcinoma diagnosis. J Proteome Res. 2019;18(9):3305–3316. doi:10.1021/acs.jproteome.9b0024231310545
   PubMed Web of Science ®Google Scholar
• Achkar JM, Cortes L, Croteau P, et al. Host protein biomarkers identify active tuberculosis in HIV uninfected and co-infected individuals. EBioMedicine. 2015;2(9):1160–1168. doi:10.1016/j.ebiom.2015.07.03926501113
   PubMed Web of Science ®Google Scholar
• Xu DD, Deng DF, Li X, et al. Discovery and identification of serum potential biomarkers for pulmonary tuberculosis using iTRAQ-coupled two-dimensional LC-MS/MS. Proteomics. 2014;14(2–3):322–331. doi:10.1002/pmic.20130038324339194
   PubMed Web of Science ®Google Scholar
• Chen C, Yan T, Liu L, Wang J, Jin Q. Identification of a novel serum biomarker for tuberculosis infection in Chinese HIV patients by iTRAQ-based quantitative proteomics. Front Microbiol. 2018;9:330. doi:10.3389/fmicb.2018.0033029535695
   PubMed Web of Science ®Google Scholar
• Jayakumar A, Vittinghoff E, Segal MR, et al. Serum biomarkers of treatment response within a randomized clinical trial for pulmonary tuberculosis. Tuberculosis (Edinb). 2015;95(4):415–420. doi:10.1016/j.tube.2015.04.01126022314
   PubMed Web of Science ®Google Scholar
• Johnson JL, Geldenhuys H, Thiel BA, et al. Effect of isoniazid therapy for latent TB infection on QuantiFERON-TB gold in-tube responses in adults with positive tuberculin skin test results in a high TB Incidence area. Chest. 2014;145(3):612–617. doi:10.1378/chest.13-123224135768
   PubMed Web of Science ®Google Scholar
• Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol. 2018;14(8):e8126. doi:10.15252/msb.2017812630104418
   PubMed Web of Science ®Google Scholar
• Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674–3676. doi:10.1093/bioinformatics/bti61016081474
   PubMed Web of Science ®Google Scholar
• Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35(WebServer issue):W182–W185. doi:10.1093/nar/gkm32117526522
   PubMed Web of Science ®Google Scholar
• Lange C, Chesov D, Heyckendorf J, Leung CC, Udwadia Z, Dheda K. Drug-resistant tuberculosis: an update on disease burden, diagnosis and treatment. Respirology. 2018;23(7):656–673. doi:10.1111/resp.1330429641838
   PubMed Web of Science ®Google Scholar
• Hu A, Noble WS, Wolf-Yadlin A. Technical advances in proteomics: new developments in data-independent acquisition. F1000Res. 2016;5:419. doi:10.12688/f1000research.7042.1
   Google Scholar
• Bruderer R, Bernhardt OM, Gandhi T, et al. Optimization of experimental parameters in data-independent mass spectrometry significantly increases depth and reproducibility of results. Mol Cell Proteomics. 2017;16(12):2296–2309. doi:10.1074/mcp.RA117.00031429070702
   PubMed Web of Science ®Google Scholar
• Liu Y, Huttenhain R, Collins B, Aebersold R. Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Rev Mol Diagn. 2013;13(8):811–825. doi:10.1586/14737159.2013.84508924138574
   PubMed Web of Science ®Google Scholar
• Carlyle BC, Trombetta BA, Arnold SE. Proteomic approaches for the discovery of biofluid biomarkers of neurodegenerative dementias. Proteomes. 2018;6(3):32. doi:10.3390/proteomes6030032
   PubMed Web of Science ®Google Scholar
• Tong L, Tergaonkar V. Rho protein GTPases and their interactions with NFkappaB: crossroads of inflammation and matrix biology. Biosci Rep. 2014;34(3). doi:10.1042/BSR20140021
   Web of Science ®Google Scholar
• Zanoni I, Granucci F. Role of CD14 in host protection against infections and in metabolism regulation. Front Cell Infect Microbiol. 2013;3:32. doi:10.3389/fcimb.2013.0003223898465
   PubMed Web of Science ®Google Scholar
• Rosas-Taraco AG, Revol A, Salinas-Carmona MC, Rendon A, Caballero-Olin G, Arce-Mendoza AY. CD14 C(−159)T polymorphism is a risk factor for development of pulmonary tuberculosis. J Infect Dis. 2007;196(11):1698–1706. doi:10.1086/52214718008256
   PubMed Web of Science ®Google Scholar
• Lawn SD, Labeta MO, Arias M, Acheampong JW, Griffin GE. Elevated serum concentrations of soluble CD14 in HIV- and HIV+ patients with tuberculosis in Africa: prolonged elevation during anti-tuberculosis treatment. Clin Exp Immunol. 2000;120(3):483–487. doi:10.1046/j.1365-2249.2000.01246.x10844527
   PubMed Web of Science ®Google Scholar
• Wieland CW, van der Windt GJ, Wiersinga WJ, Florquin S, van der Poll T. CD14 contributes to pulmonary inflammation and mortality during murine tuberculosis. Immunology. 2008;125(2):272–279. doi:10.1111/j.1365-2567.2008.02840.x18393969
   PubMed Web of Science ®Google Scholar
• Heung LJ, Luberto C, Del Poeta M. Role of sphingolipids in microbial pathogenesis. Infect Immun. 2006;74(1):28–39. doi:10.1128/IAI.74.1.28-39.200616368954
   PubMed Web of Science ®Google Scholar
• Niekamp P, Guzman G, Leier H, et al. Sphingomyelin biosynthesis is critical in organizing phosphoinositide turnover during phagocytic uptake of Mycobacterium tuberculosis. bioRxiv. 2019;565226.
   Google Scholar
• Cruz D, Watson AD, Miller CS, et al. Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy. J Clin Invest. 2008;118(8):2917–2928. doi:10.1172/JCI3418918636118
   PubMed Web of Science ®Google Scholar
• Ramakrishnan K, Shenbagarathai R, Kavitha K, Thirumalaikolundusubramanian P, Rathinasabapati R. Selenium levels in persons with HIV/tuberculosis in India, Madurai City. Clin Lab. 2012;58(1–2):165–168.22372360
   PubMed Web of Science ®Google Scholar
• Grobler L, Nagpal S, Sudarsanam TD, Sinclair D. Nutritional supplements for people being treated for active tuberculosis. Cochrane Database Syst Rev. 2016;6.
   Google Scholar
• Lee J, Geddes K, Streutker C, Philpott DJ, Girardin SE. Role of mouse peptidoglycan recognition protein PGLYRP2 in the innate immune response to Salmonella enterica serovar Typhimurium infection in vivo. Infect Immun. 2012;80(8):2645–2654. doi:10.1128/IAI.00168-1222615249
   PubMed Web of Science ®Google Scholar
• Shi L, Jiang Q, Bushkin Y, Subbian S, Tyagi S, Garsin DA. Biphasic dynamics of macrophage immunometabolism during Mycobacterium tuberculosis Infection. MBio. 2019;10(2):2. doi:10.1128/mBio.02550-18
   Web of Science ®Google Scholar