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Biomarkers for NeuroAIDS: The Widening Scope of Metabolomics

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Abstract

“Metabolomics”, the measurement of metabolite concentrations and fluxes in cell systems, is an emerging science that has enormous potential and several unique characteristics. The current applications for this field are, primarily, toxicological profiling and biomarker studies. This review of metabolomics research highlights the identification of reliable biomarkers with emphasis on neuroAIDS. Such identification of candidate markers will be advantageous for tracking the progression of human immunodeficiency virus/central nervous system (HIV/CNS) disease to gain maximal benefit from antiretroviral treatment and to provide insight into the mechanism of related neuropathogenesis.

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References

  • Albright AV, Soldan SS, Gonzalez-Scarano F (2003) Pathogenesis of human immunodeficiency virus-induced neurological disease. J Neurovirol 9:222–227

    PubMed  CAS  Google Scholar 

  • Bligny R, Douce R (2001) NMR and plant metabolism. Curr Opin Plant Biol 4(3):191–196

    Article  PubMed  CAS  Google Scholar 

  • Bollard ME, Keun HC, Beckonert O, Ebbels TM, Antti H, Nicholls AW, Shockcor JP, Cantor GH, Stevens G, Lindon JC, Holmes E, Nicholson JK (2005) Comparative metabonomics of differential hydrazine toxicity in the rat and mouse. Toxicol Appl Pharmacol 204(2):135–151

    Article  PubMed  CAS  Google Scholar 

  • Brew BJ (2001) AIDS Demetia Complex. Oxford University Press, Oxford

    Google Scholar 

  • Castrillo JI, Hayes A, Mohammed S, Gaskell SJ, Oliver SG (2003) An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 62(6):929–937

    Article  PubMed  CAS  Google Scholar 

  • Chace DH (2001) Mass spectrometry in the clinical laboratory. Chem Rev 101(2):445–477

    Article  PubMed  CAS  Google Scholar 

  • Chace DH, Kalas TA, Naylor EW (2003) Use of tandem mass spectrometry for multianalyte screening of dried blood specimens from newborns. Clin Chem 49(11):1797–1817

    Article  PubMed  CAS  Google Scholar 

  • Chelius D, Zhang T, Wang G, Shen RF (2003) Global protein identification and quantification technology using two-dimensional liquid chromatography nanospray mass spectrometry. Anal Chem 75(23):6658–6665

    Article  PubMed  CAS  Google Scholar 

  • Conant K, Garzino-Demo A, Nath A, McArthur JC, Halliday W, Power C, Gallo RC, Major EO (1998) Induction of monocyte chemoattractant protein-1 in HIV-1 Tat-stimulated astrocytes and elevation in AIDS dementia. Proc Natl Acad Sci USA 95:3117–3121

    Article  PubMed  CAS  Google Scholar 

  • Corcoran O, Spraul M (2003) LC-NMR-MS in drug discovery. Drug Discov Today 15 8(14):624–631

    Article  CAS  Google Scholar 

  • Craig A, Sidaway J, Holmes E, Orton T, Jackson D, Rowlinson R, Nickson J, Tonge R, Wilson I, Nicholson J (2006) Systems toxicology: integrated genomic, proteomic and metabonomic analysis of methapyrilene induced hepatotoxicity in the rat. J Proteome Res 5(7):1586–1601

    Article  PubMed  CAS  Google Scholar 

  • Crockford DJ, Holmes E, Lindon JC, Plumb RS, Zirah S, Bruce SJ, Rainville P, Stumpf CL, Nicholson JK (2006) Statistical heterospectroscopy, an approach to the integrated analysis of NMR and UPLC-MS data sets: application in metabonomic toxicology studies. Anal Chem 78(2):363–371

    Article  PubMed  CAS  Google Scholar 

  • Cysique LA, Brew BJ, Halman M, Catalan J, Sacktor N, Price RW, Brown S, Atkinson JH, Clifford DB, Simpson D, Torres G, Hall C, Power C, Marder K, McArthur JC, Symonds W, Romero C (2005) Undetectable cerebrospinal fluid HIV RNA and beta-2 microglobulin do not indicate inactive AIDS dementia complex in highly active antiretroviral therapy-treated patients. J Acquir Immune Defic Syndr 39:426–429

    Article  PubMed  CAS  Google Scholar 

  • Dachtler M, Glaser T, Kohler K, Albert K (2001) Combined HPLC-MS and HPLC-NMR on-line coupling for the separation and determination of lutein and zeaxanthin stereoisomers in spinach and in retina. Anal Chem 73(3):667–674

    Article  PubMed  CAS  Google Scholar 

  • Davis LE, Hjelle BL, Miller VE, Palmer DL, Llewellyn AL, Merlin TL, Young SA, Mills RG, Wachsman W, Wiley CA (1992) Early viral brain invasion in iatrogenic human immunodeficiency virus infection. Neurology 42:1736–1739

    PubMed  CAS  Google Scholar 

  • Defernez M, Colquhoun IJ (2003) Factors affecting the robustness of metabolite fingerprinting using 1H NMR spectra. Phytochemistry 62(6):1009–1017

    Article  PubMed  CAS  Google Scholar 

  • Diesing TS, Swindells S, Gelbard H, Gendelman HE (2002) HIV-1-associated dementia: a basic science and clinical perspective. AIDS Read 12:358–368

    PubMed  Google Scholar 

  • Dore GJ, Correll PK, Li Y, Kaldor JM, Cooper DA, Brew BJ (1999) Changes to AIDS dementia complex in the era of highly active antiretroviral therapy. Aids 13:1249–1253

    Article  PubMed  CAS  Google Scholar 

  • Dunn WB, Bailey NJ, Johnson HE (2005) Measuring the metabolome: current analytical technologies. Analyst 130(5):606–25

    Article  PubMed  CAS  Google Scholar 

  • Ellis RJ, Moore DJ, Childers ME, Letendre S, McCutchan JA, Wolfson T, Spector SA, Hsia K, Heaton RK, Grant I (2002) Progression to neuropsychological impairment in human immunodeficiency virus infection predicted by elevated cerebrospinal fluid levels of human immunodeficiency virus RNA. Arch Neurol 59:923–928

    Article  PubMed  Google Scholar 

  • Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, Willmitzer L (2000) Metabolite profiling for plant functional genomics. Nat Biotechnol 18(11):1157–1161

    Article  PubMed  CAS  Google Scholar 

  • Fox HS, Gold LH, Henriksen SJ, Bloom FE (1997) Simian immunodeficiency virus: a model for neuroAIDS. Neurobiol Dis 4:265–274

    Article  PubMed  CAS  Google Scholar 

  • Frank R, Hargreaves R (2003) Clinical biomarkers in drug discovery and development. Nat Rev Drug Discov 2:566–580

    Article  PubMed  CAS  Google Scholar 

  • Gangl ET, Annan MM, Spooner N, Vouros P (2001) Reduction of signal suppression effects in ESI-MS using a nanosplitting device. Anal Chem 73(23):5635–5644

    Article  PubMed  CAS  Google Scholar 

  • Gartner S (2000) HIV infection and dementia. Science 287:602–604

    Article  PubMed  CAS  Google Scholar 

  • Gendelman HE, Lipton SA, Tardieu M, Bukrinsky MI, Nottet HS (1994) The neuropathogenesis of HIV-1 infection. J Leukoc Biol 56:389–398

    PubMed  CAS  Google Scholar 

  • Gray F, Hurtrel M, Hurtrel B (1993) Early central nervous system changes in human immunodeficiency virus (HIV)-infection. Neuropathol Appl Neurobiol 19:3–9

    PubMed  CAS  Google Scholar 

  • Gray F, Chretien F, Vallat-Decouvelaere AV, Scaravilli F (2003) The changing pattern of HIV neuropathology in the HAART era. J Neuropathol Exp Neurol 62:429–440

    PubMed  Google Scholar 

  • Griffin JL, Williams HJ, Sang E, Clarke K, Rae C, Nicholson JK (2001) Metabolic profiling of genetic disorders: a multitissue (1)H nuclear magnetic resonance spectroscopic and pattern recognition study into dystrophic tissue. Anal Biochem 293(1):16–21

    Article  PubMed  CAS  Google Scholar 

  • Griffiths WJ, Liu S, Yang Y, Purdy RH, Sjovall J (1999) Nano-electrospray tandem mass spectrometry for the analysis of neurosteroid sulphates. Rapid Commun Mass Spectrom 13(15):1595–1610

    Article  PubMed  CAS  Google Scholar 

  • Holmes E, Tsang TM, Tabrizi SJ (2006) The application of NMR-based metabonomics in neurological disorders. NeuroRx 3(3):358–372

    Article  PubMed  CAS  Google Scholar 

  • Horning EC, Horning MG (1971) Metabolic profiles: gas-phase methods for analysis of metabolites. Clin Chem 17:802–809

    PubMed  CAS  Google Scholar 

  • Kanehisa M (2002) The KEGG database. Novartis Found Symp. 247:91–101; discussion 101–103, 119–128, 244–252

  • Katajamaa M, Oresic M (2005) Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics 6:179

    Article  PubMed  CAS  Google Scholar 

  • Katajamaa M, Miettinen J, Oresic M (2006) MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22(5):634–636

    Article  PubMed  CAS  Google Scholar 

  • Kaul M, Garden GA, Lipton SA (2001) Pathways to neuronal injury and apoptosis in HIV-associated dementia. Nature 410:988–994

    Article  PubMed  CAS  Google Scholar 

  • Kelder W, McArthur JC, Nance-Sproson T, McClernon D, Griffin DE (1998) Beta-chemokines MCP-1 and RANTES are selectively increased in cerebrospinal fluid of patients with human immunodeficiency virus-associated dementia. Ann Neurol 44:831–835

    Article  PubMed  CAS  Google Scholar 

  • Kolb SA, Sporer B, Lahrtz F, Koedel U, Pfister HW, Fontana A (1999) Identification of a T cell chemotactic factor in the cerebrospinal fluid of HIV-1-infected individuals as interferon-gamma inducible protein 10. J Neuroimmunol 93:172–181

    Article  PubMed  CAS  Google Scholar 

  • Kuhara T (2005) Gas chromatographic-mass spectrometric urinary metabolome analysis to study mutations of inborn errors of metabolism. Mass Spectrom Rev 24(6):814–827

    Article  PubMed  CAS  Google Scholar 

  • Lane TE, Buchmeier MJ, Watry DD, Fox HS (1996) Expression of inflammatory cytokines and inducible nitric oxide synthase in brains of SIV-infected rhesus monkeys: applications to HIV-induced central nervous system disease. Mol Med 2:27–37

    PubMed  CAS  Google Scholar 

  • Lenz EM, Bright J, Knight R, Westwood FR, Davies D, Major H, Wilson ID (2005) Metabonomics with 1H-NMR spectroscopy and liquid chromatography-mass spectrometry applied to the investigation of metabolic changes caused by gentamicin-induced nephrotoxicity in the rat. Biomarkers 10(2–3):173–187

    Article  PubMed  CAS  Google Scholar 

  • Lutz U, Lutz RW, Lutz WK (2006) Metabolic profiling of glucuronides in human urine by LC-MS/MS and partial least-squares discriminant analysis for classification and prediction of gender. Anal Chem 78(13):4564–4571

    Article  PubMed  CAS  Google Scholar 

  • Ma S, Chowdhury SK, Alton KB (2006) Application of mass spectrometry for metabolite identification. Curr Drug Metab 7(5):503–523

    Article  PubMed  CAS  Google Scholar 

  • Mankowski JL, Clements JE, Zink MC (2002) Searching for clues: tracking the pathogenesis of human immunodeficiency virus central nervous system disease by use of an accelerated, consistent simian immunodeficiency virus macaque model. J Infect Dis 186 (Suppl) 2:S199–S208

    Article  PubMed  Google Scholar 

  • Marcondes MC, Burudi EM, Huitron-Resendiz S, Sanchez-Alavez M, Watry D, Zandonatti M, Henriksen SJ, Fox HS (2001) Highly activated CD8(+) T cells in the brain correlate with early central nervous system dysfunction in simian immunodeficiency virus infection. J Immunol 167:5429–5438

    PubMed  CAS  Google Scholar 

  • Masliah E, DeTeresa RM, Mallory ME, Hansen LA (2000) Changes in pathological findings at autopsy in AIDS cases for the last 15 years. Aids 14:69–74

    Article  PubMed  CAS  Google Scholar 

  • Masliah E, Roberts ES, Langford D, Everall I, Crews L, Adame A, Rockenstein E, Fox HS (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. J Neuroimmunol 157:163–175

    Article  PubMed  CAS  Google Scholar 

  • Mastroianni CM, Paoletti F, Valenti C, Vullo V, Jirillo E, Delia S (1992) Tumour necrosis factor (TNF-alpha) and neurological disorders in HIV infection. J Neurol Neurosurg Psychiatry 55:219–221

    Article  PubMed  CAS  Google Scholar 

  • Matsumoto I, Kuhara T (1996) A new chemical diagnostic method for inborn errors of metabolism by mass spectrometry—rapid, practical and simultaneous urinary metabolites analysis. Mass Spectrom Rev 15:43–57

    Article  Google Scholar 

  • Maurer HH (2005) Advances in analytical toxicology: the current role of liquid chromatography-mass spectrometry in drug quantification in blood and oral fluid. Anal Bioanal Chem 381(1):110–118

    Article  PubMed  CAS  Google Scholar 

  • McArthur JC, Haughey N, Gartner S, Conant K, Pardo C, Nath A, Sacktor N (2003) Human immunodeficiency virus-associated dementia: an evolving disease. J Neurovirol 9:205–221

    PubMed  CAS  Google Scholar 

  • Nicholson JK, Connelly J, Lindon JC, Holmes E (2002) Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov 1:153–161

    Article  PubMed  CAS  Google Scholar 

  • Nordstrom A, O’maille G, Qin C, Siuzdak G (2006) Nonlinear data alignment for UPLC-MS and HPLC-MS based metabolomics: quantitative analysis of endogenous and exogenous metabolites in human serum. Anal Chem 78(10):3289–3295

    Article  PubMed  CAS  Google Scholar 

  • Nuovo GJ, Alfieri ML (1996) AIDS dementia is associated with massive, activated HIV-1 infection and concomitant expression of several cytokines. Mol Med 2:358–366

    Article  PubMed  CAS  Google Scholar 

  • Olson DL, Norcross JA, O’Neil-Johnson M, Molitor PF, Detlefsen DJ, Wilson AG, Peck TL (2004) Microflow NMR: concepts and capabilities. Anal Chem 76(10):2966–2974

    Article  PubMed  CAS  Google Scholar 

  • Plumb RS, Warwick H, Higton D, Dear GJ, Mallett DN (2001) Determination of 4-hydroxytamoxifen in mouse plasma in the pg/mL range by gradient capillary liquid chromatography/tandem mass spectrometry. Rapid Commun Mass Spectrom 15(4):297–303

    Article  PubMed  CAS  Google Scholar 

  • Plumb R, Castro-Perez J, Granger J, Beattie I, Joncour K, Wright A (2004) Ultra-performance liquid chromatography coupled to quadrupole-orthogonal time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 18(19):2331–2337

    Article  PubMed  CAS  Google Scholar 

  • Ratcliffe RG, Shachar-Hill Y (2001) Probing plant metabolism with NMR. Annu Rev Plant Physiol Plant Mol Biol 52:499–526

    Article  PubMed  CAS  Google Scholar 

  • Rausch DM, Murray EA, Eiden LE (1999) The SIV-infected rhesus monkey model for HIV-associated dementia and implications for neurological diseases. J Leukoc Biol 65:466–474

    PubMed  CAS  Google Scholar 

  • Reo NV (2002) NMR-based metabolomics. Drug Chem Toxicol 25(4):375–382

    Article  PubMed  CAS  Google Scholar 

  • Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen SJ, Taffe MA, Fox HS (2003) Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol 162:2041–2057

    PubMed  CAS  Google Scholar 

  • Roberts ES, Burudi EM, Flynn C, Madden LJ, Roinick KL, Watry DD, Zandonatti MA, Taffe MA, Fox HS (2004) Acute SIV infection of the brain leads to upregulation of IL6 and interferon-regulated genes: expression patterns throughout disease progression and impact on neuroAIDS. J Neuroimmunol 157:81–92

    Article  PubMed  CAS  Google Scholar 

  • Roberts ES, Huitron-Resendiz S, Taffe MA, Marcondes MC, Flynn CT, Lanigan CM, Hammond JA, Head SR, Henriksen SJ, Fox HS (2006) Host response and dysfunction in the CNS during chronic simian immunodeficiency virus infection. J Neurosci 26:4577–4585

    Article  PubMed  CAS  Google Scholar 

  • Sevigny JJ, Albert SM, McDermott MP, McArthur JC, Sacktor N, Conant K, Schifitto G, Selnes OA, Stern Y, McClernon DR, Palumbo D, Kieburtz K, Riggs G, Cohen B, Epstein LG, Marder K (2004) Evaluation of HIV RNA and markers of immune activation as predictors of HIV-associated dementia. Neurology 63:2084–2090

    PubMed  CAS  Google Scholar 

  • Sharer LR, Baskin GB, Cho ES, Murphey-Corb M, Blumberg BM, Epstein LG (1988) Comparison of simian immunodeficiency virus and human immunodeficiency virus encephalitides in the immature host. Ann Neurol 23 (Suppl):S108–S112

    Article  PubMed  Google Scholar 

  • Sharer LR (1992) Pathology of HIV-1 infection of the central nervous system. A review. J Neuropathol Exp Neurol 51:3–11

    PubMed  CAS  Google Scholar 

  • Siuzdak G (2006) The Expanding Role of Mass Spectrometry in Biotechnology, 2nd edn. MCC Press, San Diego, pp 1–252

    Google Scholar 

  • Smith CA, O’Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G (2005) METLIN: a metabolite mass spectral database. Ther Drug Monit 27(6):747–751

    Article  PubMed  CAS  Google Scholar 

  • Smith CA, Want EJ, O’Maille G, Abagyan R, Siuzdak G (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification. Anal Chem 78:779–787

    Article  PubMed  CAS  Google Scholar 

  • Spraul M, Freund AS, Nast RE, Withers RS, Maas WE, Corcoran O (2003) Advancing NMR sensitivity for LC-NMR-MS using a cryoflow probe: application to the analysis of acetaminophen metabolites in urine. Anal Chem 75(6):1536–1541

    Article  PubMed  CAS  Google Scholar 

  • Tang H, Wang Y, Nicholson JK, Lindon JC (2004) Use of relaxation-edited one-dimensional and two dimensional nuclear magnetic resonance spectroscopy to improve detection of small metabolites in blood plasma. Anal Biochem 325(2):260–272

    Article  PubMed  CAS  Google Scholar 

  • Voyksner RD (1997) Combining liquid chromatography with electospray mass spectrometry. In: Cole RB (ed) Electrospray Ionization Mass Spectrometry. Wiley, New York, pp 323–341

    Google Scholar 

  • Williams K, Alvarez X, Lackner AA (2001) Central nervous system perivascular cells are immunoregulatory cells that connect the CNS with the peripheral immune system. Glia 36:156–164.

    Article  PubMed  CAS  Google Scholar 

  • Wilson ID, Plumb R, Granger J, Major H, Williams R, Lenz EM (2005a) HPLC-MS-based methods for the study of metabonomics. J Chromatogr B Anal Technol Biomed Life Sci 817(1):67–76

    CAS  Google Scholar 

  • Wilson ID, Nicholson JK, Castro-Perez J, Granger JH, Johnson KA, Smith BW, Plumb RS (2005b) High resolution “ultra performance” liquid chromatography coupled to oa-TOF mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies. J Proteome Res 4(2): 591–598

    Article  PubMed  CAS  Google Scholar 

  • Wolff JC, Eckers C, Sage AB, Giles K, Bateman R (2001) Accurate mass liquid chromatography/mass spectrometry on quadrupole orthogonal acceleration time-of-flight mass analyzers using switching between separate sample and reference sprays. 2. Applications using the dual-electrospray ion source. Anal Chem 73(11):2605–2612

    Article  PubMed  CAS  Google Scholar 

  • Yang Z (2006) Online hyphenated liquid chromatography-nuclear magnetic resonance spectroscopy-mass spectrometry for drug metabolite and nature product analysis. J Pharm Biomed Anal 40(3):516–527

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

Our work on biomarkers in neuroAIDS is supported by NIH grants MH073490 and MH062261. This is manuscript number 18317 from The Scripps Research Institute.

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Correspondence to Howard S. Fox.

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Pendyala, G., Want, E.J., Webb, W. et al. Biomarkers for NeuroAIDS: The Widening Scope of Metabolomics. Jrnl Neuroimmune Pharm 2, 72–80 (2007). https://doi.org/10.1007/s11481-006-9041-3

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