Host-based peripheral blood gene expression analysis for diagnosis of infectious diseases

Journal of Clinical Microbiology

Volumn 55, Issue 2, 2017, Pages 360-368

  Holcomb, Zachary E ^a   Tsalik, Ephraim L ^a,b,c   Woods, Christopher W ^a,b,c   McClain, Micah T ^a,b,c  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

^c DURHAM VA MEDICAL CENTER   (United States)

Author keywords

Diagnostics; Gene expression

Indexed keywords

BIOLOGICAL MARKER; MESSENGER RNA;

ANTHRAX; ARTICLE; BACTERIAL INFECTION; BRUCELLOSIS; CANDIDIASIS; DIAGNOSTIC ACCURACY; DISEASE CLASSIFICATION; ESCHERICHIA COLI INFECTION; GENE EXPRESSION ASSAY; HOST BASED PERIPHERAL BLOOD GENE EXPRESSION ANALYSIS; HOST PATHOGEN INTERACTION; HUMAN; INFECTION; MICROARRAY ANALYSIS; MYCOSIS; NONHUMAN; PATIENT CARE; PATIENT CODING; PLAGUE; PNEUMOCOCCAL INFECTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; SEPSIS; STAPHYLOCOCCUS INFECTION; STUDY DESIGN; TULAREMIA; VIRAL RESPIRATORY TRACT INFECTION; VIRUS INFECTION; COMMUNICABLE DISEASES; GENE EXPRESSION PROFILING; IMMUNOLOGY; LEUKOCYTE; MOLECULAR DIAGNOSIS; PATHOLOGY; PROCEDURES;

COMMUNICABLE DISEASES; GENE EXPRESSION PROFILING; HUMANS; LEUKOCYTES; MOLECULAR DIAGNOSTIC TECHNIQUES;

EID: 85011990304     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.01057-16     Document Type: Article

References (28)

1. Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S. 2009. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459: 1122-1125. https://doi.org/10.1038/nature08182.
2. Waugh TR. 1923. The blood sedimentation test; its history, technique, nature and clinical application. Can Med Assoc J 13:604-608.
3. Tillett WS, Francis T. 1930. Serological reactions in pneumonia with a non-protein somatic fraction of pneumococcus. J Exp Med 52:561-571. https://doi.org/10.1084/jem.52.4.561.
4. Assicot M, Gendrel D, Carsin H, Raymond J, Guilbaud J, Bohuon C. 1993. High serum procalcitonin concentrations in patients with sepsis and infection. Lancet 341:515-518. https://doi.org/10.1016/0140-6736 (93)90277-N.
5. Christ-Crain M, Jaccard-Stolz D, Bingisser R, Gencay MM, Huber PR, Tamm M, Muller B. 2004. Effect of procalcitonin-guided treatment on antibiotic use and outcome in lower respiratory tract infections: Clusterrandomised, single-blinded intervention trial. Lancet 363:600-607. https://doi.org/10.1016/S0140-6736(04)15591-8.
6. Ettinger M, Calliess T, Kielstein JT, Sibai J, Bruckner T, Lichtinghagen R, Windhagen H, Lukasz A. 2015. Circulating biomarkers for discrimination between aseptic joint failure, low-grade infection, and high-grade septic failure. Clin Infect Dis 61:332-341. https://doi.org/10.1093/cid/civ286.
7. Petri MG, Konig J, Moecke HP, Gramm HJ, Barkow H, Kujath P, Dennhart R, Schafer H, Meyer N, Kalmar P, Thulig P, Muller J, Lode H. 1997. Epidemiology of invasive mycosis in ICU patients: A prospective multicenter study in 435 non-neutropenic patients. Paul-Ehrlich Society for Chemotherapy, Divisions of Mycology and Pneumonia Research. Intensive Care Med 23:317-325. https://doi.org/10.1007/s001340050334.
8. Ramilo O, Allman W, Chung W, Mejias A, Ardura M, Glaser C, Wittkowski KM, Piqueras B, Banchereau J, Palucka AK, Chaussabel D. 2007. Gene expression patterns in blood leukocytes discriminate patients with acute infections. Blood 109:2066-2077. https://doi.org/10.1182/blood-2006-02-002477.
9. Woods CW, McClain MT, Chen M, Zaas AK, Nicholson BP, Varkey J, Veldman T, Kingsmore SF, Huang Y, Lambkin-Williams R, Gilbert AG, Hero AO, III, Ramsburg E, Glickman S, Lucas JE, Carin L, Ginsburg GS. 2013. A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2. PLoS One 8:e52198. https://doi.org/10.1371/journal.pone.0052198.
10. Zaas AK, Burke T, Chen M, McClain M, Nicholson B, Veldman T, Tsalik EL, Fowler V, Rivers EP, Otero R, Kingsmore SF, Voora D, Lucas J, Hero AO, Carin L, Woods CW, Ginsburg GS. 2013. A host-based RT-PCR gene expression signature to identify acute respiratory viral infection. Sci Transl Med 5:203ra126. https://doi.org/10.1126/scitranslmed.3006280.
11. Baginsky S, Hennig L, Zimmermann P, Gruissem W. 2010. Gene expression analysis, proteomics, and network discovery. Plant Physiol 152: 402-410. https://doi.org/10.1104/pp.109.150433.
12. Carvalho CM, Chang J, Lucas JE, Nevins JR, Wang Q, West M. 2008. High-dimensional sparse factor modeling: Applications in gene expression genomics. J Am Stat Assoc 103:1438-1456. https://doi.org/10.1198/016214508000000869.
13. Chen M, Carlson D, Zaas A, Woods CW, Ginsburg GS, Hero AO, III, Lucas J, Carin L. 2011. Detection of viruses via statistical gene expression analysis. IEEE Trans Biomed Eng 58:468-479. https://doi.org/10.1109/TBME.2010.2059702.
14. McHugh L, Seldon TA, Brandon RA, Kirk JT, Rapisarda A, Sutherland AJ, Presneill JJ, Venter DJ, Lipman J, Thomas MR, Klein Klouwenberg PM, van Vught L, Scicluna B, Bonten M, Cremer OL, Schultz MJ, van der Poll T, Yager TD, Brandon RB. 2015. A molecular host response assay to discriminate between sepsis and infection-negative systemic inflammation in critically ill patients: Discovery and validation in independent cohorts. PLoS Med 12:e1001916. https://doi.org/10.1371/journal.pmed.1001916.
15. Maslove DM, Tang BM, McLean AS. 2012. Identification of sepsis subtypes in critically ill adults using gene expression profiling. Crit Care 16:R183. https://doi.org/10.1186/cc11667.
16. Wong HR, Cvijanovich NZ, Allen GL, Thomas NJ, Freishtat RJ, Anas N, Meyer K, Checchia PA, Lin R, Shanley TP, Bigham MT, Wheeler DS, Doughty LA, Tegtmeyer K, Poynter SE, Kaplan JM, Chima RS, Stalets E, Basu RK, Varisco BM, Barr FE. 2011. Validation of a gene expressionbased subclassification strategy for pediatric septic shock. Crit Care Med 39:2511-2517. https://doi.org/10.1097/CCM.0b013e3182257675.
17. Zaas AK, Chen M, Varkey J, Veldman T, Hero AO, III, Lucas J, Huang Y, Turner R, Gilbert A, Lambkin-Williams R, Oien NC, Nicholson B, Kingsmore S, Carin L, Woods CW, Ginsburg GS. 2009. Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans. Cell Host Microbe 6:207-217. https://doi.org/10.1016/j.chom.2009.07.006.
18. Mejias A, Dimo B, Suarez NM, Garcia C, Suarez-Arrabal MC, Jartti T, Blankenship D, Jordan-Villegas A, Ardura MI, Xu Z, Banchereau J, Chaussabel D, Ramilo O. 2013. Whole blood gene expression profiles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection. PLoS Med 10:e1001549. https://doi.org/10.1371/journal.pmed.1001549.
19. Suarez NM, Bunsow E, Falsey AR, Walsh EE, Mejias A, Ramilo O. 2015. Superiority of transcriptional profiling over procalcitonin for distinguishing bacterial from viral lower respiratory tract infections in hospitalized adults. J Infect Dis 212:213-222. https://doi.org/10.1093/infdis/jiv047.
20. Tsalik EL, Henao R, Nichols M, Burke T, Ko ER, McClain MT, Hudson LL, Mazur A, Freeman DH, Veldman T, Langley RJ, Quackenbush EB, Glickman SW, Cairns CB, Jaehne AK, Rivers EP, Otero RM, Zaas AK, Kingsmore SF, Lucas J, Fowler VG, Jr, Carin L, Ginsburg GS, Woods CW. 2016. Host gene expression classifiers diagnose acute respiratory illness etiology. Sci Transl Med 8:322ra11. https://doi.org/10.1126/scitranslmed.aad6873.
21. Berry MP, Graham CM, McNab FW, Xu Z, Bloch SA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, Quinn C, Blankenship D, Dhawan R, Cush JJ, Mejias A, Ramilo O, Kon OM, Pascual V, Banchereau J, Chaussabel D, O'Garra A. 2010. An interferon-inducible neutrophildriven blood transcriptional signature in human tuberculosis. Nature 466:973-977. https://doi.org/10.1038/nature09247.
22. Zak DE, Penn-Nicholson A, Scriba TJ, Thompson E, Suliman S, Amon LM, Mahomed H, Erasmus M, Whatney W, Hussey GD, Abrahams D, Kafaar F, Hawkridge T, Verver S, Hughes EJ, Ota M, Sutherland J, Howe R, Dockrell HM, Boom WH, Thiel B, Ottenhoff TH, Mayanja-Kizza H, Crampin AC, Downing K, Hatherill M, Valvo J, Shankar S, Parida SK, Kaufmann SH, Walzl G, Aderem A, Hanekom WA. 24 March 2016. A blood RNA signature for tuberculosis disease risk: A prospective cohort study. Lancet https://doi.org/10.1016/s0140-6736(15)01316-1.
23. Bloom CI, Graham CM, Berry MP, Rozakeas F, Redford PS, Wang Y, Xu Z, Wilkinson KA, Wilkinson RJ, Kendrick Y, Devouassoux G, Ferry T, Miyara M, Bouvry D, Valeyre D, Gorochov G, Blankenship D, Saadatian M, Vanhems P, Beynon H, Vancheeswaran R, Wickremasinghe M, Chaussabel D, Banchereau J, Pascual V, Ho LP, Lipman M, O'Garra A. 2013. Transcriptional blood signatures distinguish pulmonary tuberculosis, pulmonary sarcoidosis, pneumonias and lung cancers. PLoS One 8:e70630. https://doi.org/10.1371/journal.pone.0070630.
24. Das R, Hammamieh R, Neill R, Ludwig GV, Eker S, Lincoln P, Ramamoorthy P, Dhokalia A, Mani S, Mendis C, Cummings C, Kearney B, Royaee A, Huang XZ, Paranavitana C, Smith L, Peel S, Kanesa-Thasan N, Hoover D, Lindler LE, Yang D, Henchal E, Jett M. 2008. Early indicators of exposure to biological threat agents using host gene profiles in peripheral blood mononuclear cells. BMC Infect Dis 8:104. https://doi.org/10.1186/1471-2334-8-104.
25. Paranavitana C, Pittman PR, Velauthapillai M, Zelazowska E, Dasilva L. 2008. Transcriptional profiling of Francisella tularensis infected peripheral blood mononuclear cells: A predictive tool for tularemia. FEMS Immunol Med Microbiol 54:92-103. https://doi.org/10.1111/j.1574-695X.2008.00456.x.
26. Zaas AK, Aziz H, Lucas J, Perfect JR, Ginsburg GS. 2010. Blood gene expression signatures predict invasive candidiasis. Sci Transl Med 2:21ra17. https://doi.org/10.1126/scitranslmed.3000715.
27. Cortez KJ, Lyman CA, Kottilil S, Kim HS, Roilides E, Yang J, Fullmer B, Lempicki R, Walsh TJ. 2006. Functional genomics of innate host defense molecules in normal human monocytes in response to Aspergillus fumigatus. Infect Immun 74:2353-2365. https://doi.org/10.1128/IAI.74 .4.2353-2365.2006.
28. Yamani MH, Taylor DO, Haire C, Smedira N, Starling RC. 2007. Posttransplant ischemic injury is associated with up-regulated AlloMap gene expression. Clin Transplant 21:523-525. https://doi.org/10.1111/j.1399-0012.2007.00681.x.