In an unbiased approach to biomarker discovery, we applied a highly multiplexed proteomic technology (SOMAscan, SomaLogic, Inc, Boulder, CO) to understand changes in proteins from paired serum samples at enrollment and after 8 weeks of TB treatment from 39 patients with pulmonary TB from Kampala, Uganda enrolled in the Center for Disease Control and Prevention’s Tuberculosis Trials Consortium (TBTC) Study 29. This work represents the first large-scale proteomic analysis employing modified DNA aptamers in a study of active tuberculosis (TB). We identified multiple proteins that exhibit significant expression differences during the intensive phase of TB therapy. There was enrichment for proteins in conserved networks of biological processes and function including antimicrobial defense, tissue healing and remodeling, acute phase response, pattern recognition, protease/anti-proteases, complement and coagulation cascade, apoptosis, immunity and inflammation pathways. Members of cytokine pathways such as interferon-gamma, while present, were not as highly represented as might have been predicted. The top proteins that changed between baseline and 8 weeks of therapy were TSP4, TIMP-2, SEPR, MRC-2, Antithrombin III, SAA, CRP, NPS-PLA2, LEAP-1, and LBP. The novel proteins elucidated in this work may provide new insights for understanding TB disease, its treatment and subsequent healing processes that occur in response to effective therapy.
References
[1]
Ostroff RM, Bigbee WL, Franklin W, Gold L, Mehan M, et al. (2010) Unlocking biomarker discovery: large scale application of aptamer proteomic technology for early detection of lung cancer. PloS one 5: e15003.
[2]
Gold L, Ayers D, Bertino J, Bock C, Bock A, et al. (2010) Aptamer-based multiplexed proteomic technology for biomarker discovery. PloS one 5: e15004.
[3]
Ostroff R, Foreman T, Keeney TR, Stratford S, Walker JJ, et al. (2010) The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array. Journal of proteomics 73: 649–666.
[4]
Dorman SE, Goldberg S, Stout JE, Muzanyi G, Johnson JL, et al. (2012) Substitution of rifapentine for rifampin during intensive phase treatment of pulmonary tuberculosis: Study 29 of the Tuberculosis Trials Consortium. The Journal of infectious diseases 206: 1030–1040.
[5]
Falk A, O’Connor J, Pratt P, Webb W, Wier J, et al.. (1969) Classification of pulmonary tuberculosis. Diagnostic standards and classification of tuberculosis. New York: National Tuberculosis and Respiratory Disease Association.
[6]
Kent PT, Kubica GP (1985) Public Health Mycobacteriology: A Guide for the Level III Laboratory. Atlanta, GA: Centers for Disease Control.
[7]
Zachariah R, Spielmann MP, Harries AD, Salaniponi FM (2002) Moderate to severe malnutrition in patients with tuberculosis is a risk factor associated with early death. Transactions of the Royal Society of Tropical Medicine and Hygiene 96: 291–294.
[8]
Pakasi TA, Karyadi E, Wibowo Y, Simanjuntak Y, Suratih NM, et al. (2009) Vitamin A deficiency and other factors associated with severe tuberculosis in Timor and Rote Islands, East Nusa Tenggara Province, Indonesia. European journal of clinical nutrition 63: 1130–1135.
[9]
Brody EN, Gold L (2000) Aptamers as therapeutic and diagnostic agents. Journal of biotechnology 74: 5–13.
[10]
Gold L (1995) Oligonucleotides as research, diagnostic, and therapeutic agents. The Journal of biological chemistry 270: 13581–13584.
[11]
Vaught JD, Bock C, Carter J, Fitzwater T, Otis M, et al. (2010) Expanding the chemistry of DNA for in vitro selection. Journal of the American Chemical Society 132: 4141–4151.
[12]
Storey JD (2002) A Direct Approach to False Discovery Rates. J Royal Stat Soc B 64: 479–498.
[13]
Dabney A, Storey JD, Warnes GR (2011) qvalue: Q-value estimation for false discovery rate control. R package version 1.26.0. http://CRAN.R-project.org/package=qvalue
[14]
Huang da W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research 37: 1–13.
[15]
Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols 4: 44–57.
[16]
Jiao X, Sherman BT, Huang DW, Stephens R, Baseler MW, et al. (2012) DAVID-WS: A Stateful Web Service to Facilitate Gene/Protein List Analysis. Bioinformatics 28: 1805–1806.
[17]
Mistry R, Cliff JM, Clayton CL, Beyers N, Mohamed YS, et al. (2007) Gene-expression patterns in whole blood identify subjects at risk for recurrent tuberculosis. The Journal of infectious diseases 195: 357–365.
[18]
Agranoff D, Fernandez-Reyes D, Papadopoulos MC, Rojas SA, Herbster M, et al. (2006) Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum. Lancet 368: 1012–1021.
[19]
Agarwal R, Agarwal C, Ichikawa H, Singh RP, Aggarwal BB (2006) Anticancer potential of silymarin: from bench to bed side. Anticancer research 26: 4457–4498.
[20]
Maertzdorf J, Weiner J 3rd, Mollenkopf HJ, Bauer T, Prasse A, et al. (2012) Common patterns and disease-related signatures in tuberculosis and sarcoidosis. Proceedings of the National Academy of Sciences of the United States of America.
[21]
Berry MP, Graham CM, McNab FW, Xu Z, Bloch SA, et al. (2010) An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466: 973–977.
[22]
Tanaka T, Sakurada S, Kano K, Takahashi E, Yasuda K, et al. (2011) Identification of tuberculosis-associated proteins in whole blood supernatant. BMC infectious diseases 11: 71.
[23]
Song QB, Hu WG, Wang P, Yao Y, Zeng HZ (2011) Identification of serum biomarkers for lung cancer using magnetic bead-based SELDI-TOF-MS. Acta pharmacologica Sinica 32: 1537–1542.
[24]
Wallis RS, Doherty TM, Onyebujoh P, Vahedi M, Laang H, et al. (2009) Biomarkers for tuberculosis disease activity, cure, and relapse. The Lancet infectious diseases 9: 162–172.
[25]
Nemeth J, Winkler HM, Boeck L, Adegnika AA, Clement E, et al. (2011) Specific cytokine patterns of pulmonary tuberculosis in Central Africa. Clinical immunology 138: 50–59.
[26]
Koth LL, Solberg OD, Peng JC, Bhakta NR, Nguyen CP, et al. (2011) Sarcoidosis blood transcriptome reflects lung inflammation and overlaps with tuberculosis. American journal of respiratory and critical care medicine 184: 1153–1163.
[27]
Tan SS, Ng PM, Ho B, Ding JL (2005) The antimicrobial properties of C-reactive protein (CRP). Journal of endotoxin research 11: 249–256.
[28]
Shapiro L, Pott GB, Ralston AH (2001) Alpha-1-antitrypsin inhibits human immunodeficiency virus type 1. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 15: 115–122.
[29]
Chan ED, Kaminska AM, Gill W, Chmura K, Feldman NE, et al. (2007) Alpha-1-antitrypsin (AAT) anomalies are associated with lung disease due to rapidly growing mycobacteria and AAT inhibits Mycobacterium abscessus infection of macrophages. Scandinavian journal of infectious diseases 39: 690–696.
[30]
Sow FB, Nandakumar S, Velu V, Kellar KL, Schlesinger LS, et al. (2011) Mycobacterium tuberculosis components stimulate production of the antimicrobial peptide hepcidin. Tuberculosis 91: 314–321.
[31]
Juffermans NP, Verbon A, van Deventer SJ, Buurman WA, van Deutekom H, et al. (1998) Serum concentrations of lipopolysaccharide activity-modulating proteins during tuberculosis. The Journal of infectious diseases 178: 1839–1842.
[32]
Schroder NW, Schumann RR (2005) Non-LPS targets and actions of LPS binding protein (LBP). Journal of endotoxin research 11: 237–242.
[33]
Qu XD, Lehrer RI (1998) Secretory phospholipase A2 is the principal bactericide for staphylococci and other gram-positive bacteria in human tears. Infection and immunity 66: 2791–2797.
[34]
Hunter RL (2011) Pathology of post primary tuberculosis of the lung: An illustrated critical review. Tuberculosis 91: 497–509.
[35]
Reece ST, Loddenkemper C, Askew DJ, Zedler U, Schommer-Leitner S, et al. (2010) Serine protease activity contributes to control of Mycobacterium tuberculosis in hypoxic lung granulomas in mice. The Journal of clinical investigation 120: 3365–3376.
[36]
Rajaram MV, Brooks MN, Morris JD, Torrelles JB, Azad AK, et al. (2010) Mycobacterium tuberculosis activates human macrophage peroxisome proliferator-activated receptor gamma linking mannose receptor recognition to regulation of immune responses. Journal of immunology 185: 929–942.
[37]
de la Paz Santangelo M, Gest PM, Guerin ME, Coincon M, Pham H, et al. (2011) Glycolytic and non-glycolytic functions of Mycobacterium tuberculosis fructose-1,6-bisphosphate aldolase, an essential enzyme produced by replicating and non-replicating bacilli. The Journal of biological chemistry 286: 40219–40231.
[38]
Barthel D, Singh B, Riesbeck K, Zipfel PF (2012) Haemophilus influenzae uses the surface protein E to acquire human plasminogen and to evade innate immunity. Journal of immunology 188: 379–385.
[39]
Barthel D, Schindler S, Zipfel PF (2012) Plasminogen is a complement inhibitor. The Journal of biological chemistry 287: 18831–18842.
[40]
Wu M, Aung H, Hirsch CS, Toossi Z (2012) Inhibition of Mycobacterium tuberculosis-induced signalling by transforming growth factor-beta in human mononuclear phagocytes. Scandinavian journal of immunology 75: 301–304.
[41]
Sato J, Schorey J, Ploplis VA, Haalboom E, Krahule L, et al. (2003) The fibrinolytic system in dissemination and matrix protein deposition during a mycobacterium infection. The American journal of pathology 163: 517–531.
[42]
Salgame P (2011) MMPs in tuberculosis: granuloma creators and tissue destroyers. The Journal of clinical investigation 121: 1686–1688.
[43]
Frolova EG, Sopko N, Blech L, Popovic ZB, Li J, et al.. (2012) Thrombospondin-4 regulates fibrosis and remodeling of the myocardium in response to pressure overload. FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[44]
Mustonen E, Ruskoaho H, Rysa J (2012) Thrombospondin-4, tumour necrosis factor-like weak inducer of apoptosis (TWEAK) and its receptor Fn14: Novel extracellular matrix modulating factors in cardiac remodelling. Annals of medicine.
[45]
Pohjolainen V, Mustonen E, Taskinen P, Napankangas J, Leskinen H, et al. (2012) Increased thrombospondin-2 in human fibrosclerotic and stenotic aortic valves. Atherosclerosis 220: 66–71.
[46]
Calzada MJ, Zhou L, Sipes JM, Zhang J, Krutzsch HC, et al. (2004) Alpha4beta1 integrin mediates selective endothelial cell responses to thrombospondins 1 and 2 in vitro and modulates angiogenesis in vivo. Circulation research 94: 462–470.
[47]
Paulissen G, Rocks N, Gueders MM, Crahay C, Quesada-Calvo F, et al. (2009) Role of ADAM and ADAMTS metalloproteinases in airway diseases. Respiratory research 10: 127.
[48]
Rivera-Marrero CA, Schuyler W, Roser S, Roman J (2000) Induction of MMP-9 mediated gelatinolytic activity in human monocytic cells by cell wall components of Mycobacterium tuberculosis. Microbial pathogenesis 29: 231–244.
[49]
Hrabec E, Strek M, Zieba M, Kwiatkowska S, Hrabec Z (2002) Circulation level of matrix metalloproteinase-9 is correlated with disease severity in tuberculosis patients. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 6: 713–719.
[50]
Friedland JS, Shaw TC, Price NM, Dayer JM (2002) Differential regulation of MMP-1/9 and TIMP-1 secretion in human monocytic cells in response to Mycobacterium tuberculosis. Matrix biology : journal of the International Society for Matrix Biology 21: 103–110.
[51]
Anand SP, Selvaraj P (2009) Effect of 1, 25 dihydroxyvitamin D(3) on matrix metalloproteinases MMP-7, MMP-9 and the inhibitor TIMP-1 in pulmonary tuberculosis. Clinical immunology 133: 126–131.
[52]
Maretti-Mira AC, de Pinho Rodrigues KM, de Oliveira-Neto MP, Pirmez C, Craft N (2011) MMP-9 activity is induced by Leishmania braziliensis infection and correlates with mucosal leishmaniasis. Acta tropica 119: 160–164.
[53]
Vatansever S, Gelisgen R, Uzun H, Yurt S, Kosar F (2009) Potential role of matrix metalloproteinase-2,-9 and tissue inhibitors of metalloproteinase-1,-2 in exudative pleural effusions. Clinical and investigative medicine Medecine clinique et experimentale 32: E293–300.
[54]
Taylor JL, Hattle JM, Dreitz SA, Troudt JM, Izzo LS, et al. (2006) Role for matrix metalloproteinase 9 in granuloma formation during pulmonary Mycobacterium tuberculosis infection. Infection and immunity 74: 6135–6144.
[55]
Juncker-Jensen A, Lund L (2011) Phenotypic Overlap between MMP-13 and the Plasminogen Activation System during Wound Healing in Mice. PlosOne 6.
[56]
Cardone P (2011) A Spotlight on Liquifaction: evidence from clinical settings and experimental models in tuberculosis. Clinical and Developmental Immunology 2011: 1–9.
[57]
Marquis JF, Nantel A, LaCourse R, Ryan L, North RJ, et al. (2008) Fibrotic response as a distinguishing feature of resistance and susceptibility to pulmonary infection with Mycobacterium tuberculosis in mice. Infection and immunity 76: 78–88.
[58]
Weiner J 3rd, Parida SK, Maertzdorf J, Black GF, Repsilber D, et al (2012) Biomarkers of inflammation, immunosuppression and stress with active disease are revealed by metabolomic profiling of tuberculosis patients. PloS one 7: e40221.
[59]
Ma YJ, Doni A, Skjoedt MO, Honore C, Arendrup M, et al. (2011) Heterocomplexes of mannose-binding lectin and the pentraxins PTX3 or serum amyloid P component trigger cross-activation of the complement system. The Journal of biological chemistry 286: 3405–3417.
[60]
Shibuya M (2008) Vascular endothelial growth factor-dependent and -independent regulation of angiogenesis. BMB reports 41: 278–286.
[61]
Hoheisel G, Roth M, Chan CH, Tsakiris DA, Fehr B, et al. (1997) Procoagulant activity of purified protein derivative-stimulated pleural effusion mononuclear cells in tuberculous pleurisy. Respiration; international review of thoracic diseases 64: 152–158.
[62]
Smit van Dixhoorn MG, Munir R, Sussman G, Stad R, de Haan M, et al. (2008) Gene expression profiling of suppressor mechanisms in tuberculosis. Molecular immunology 45: 1573–1586.
[63]
Weijer S, Wieland CW, Florquin S, van der Poll T (2005) A thrombomodulin mutation that impairs activated protein C generation results in uncontrolled lung inflammation during murine tuberculosis. Blood 106: 2761–2768.
[64]
Aranday-Cortes E, Hogarth PJ, Kaveh DA, Whelan AO, Villarreal-Ramos B, et al. (2012) Transcriptional profiling of disease-induced host responses in bovine tuberculosis and the identification of potential diagnostic biomarkers. PloS one 7: e30626.
[65]
Basaraba RJ (2008) Experimental tuberculosis: the role of comparative pathology inthe discovery of improved tuberculosis treatment strategies. Tuberculosis 88: S35–47.
[66]
Armstrong LC, Bjorkblom B, Hankenson KD, Siadak AW, Stiles CE, et al. (2002) Thrombospondin 2 inhibits microvascular endothelial cell proliferation by a caspase-independent mechanism. Molecular biology of the cell 13: 1893–1905.
[67]
Akhmetshina A, Palumbo K, Dees C, Bergmann C, Venalis P, et al. (2012) Activation of canonical Wnt signalling is required for TGF-beta-mediated fibrosis. Nature communications 3: 735.
[68]
Eickhoff M, Thalmann J, Hess S, Martin M, Laue T, et al. (2007) Host cell responses to Chlamydia pneumoniae in gamma interferon-induced persistence overlap those of productive infection and are linked to genes involved in apoptosis, cell cycle, and metabolism. Infection and immunity 75: 2853–2863.
[69]
Zhang YM, Fang YD, Wang YC, Wang SL, Lei ZY, et al. (2011) Role of serum amyloid P in skin graft survival and wound healing in burned patients receiving skin grafts. Clinica chimica acta; international journal of clinical chemistry 412: 227–229.
[70]
Odrowaz-Sypniewska G (2007) Markers of pro-inflammatory and pro-thrombotic state in the diagnosis of metabolic syndrome. Advances in medical sciences 52: 246–250.
[71]
Sood A, Qualls C, Schuyler M, Thyagarajan B, Steffes MW, et al.. (2012) Low Serum Adiponectin Predicts Future Risk for Asthma in Women. American journal of respiratory and critical care medicine.
[72]
Schwanhausser B, Busse D, Na L, Dittmar G, Schuchhardt J, et al. (2011) Global quantification of mammalian gene expression control. Naure 473: 337–342.
[73]
Rae JM, Johnson MD, Lippman ME, Flockhart DA (2001) Rifampin is a selective, pleiotropic inducer of drug metabolism genes in human hepatocytes: studies with cDNA and oligonucleotide expression arrays. The Journal of pharmacology and experimental therapeutics 299: 849–857.
[74]
Marrer E, Dieterle F (2010) Impact of biomarker development on drug safety assessment. Toxicology and applied pharmacology 243: 167–179.
[75]
Sigdel TK, Sarwal MM (2008) The proteogenomic path towards biomarker discovery. Pediatric transplantation 12: 737–747.
