Genome-Wide Sequencing of Cellular microRNAs Identifies a Combinatorial Expression Signature Diagnostic of Sepsis

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Ma, Yuqian ^a,b   Vilanova, David ^c   Atalar, Kerem ^a,b   Delfour, Olivier ^c   Edgeworth, Jonathan ^b   Ostermann, Marlies ^b   Hernandez Fuentes, Maria ^a,b   Razafimahatratra, Sandrine ^c   Michot, Bernard ^c   Persing, David H ^d   Ziegler, Ingrid ^e   Törös, Bianca ^e   Mölling, Paula ^e   Olcén, Per ^e   Beale, Richard ^a,b   Lord, Graham M ^a,b  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b GUY'S AND ST THOMAS' NHS FOUNDATION TRUST   (United Kingdom)

^c Cepheid Europe ^*  (France)

^d CEPHEID   (United States)

^e ÖREBRO UNIVERSITY HOSPITAL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; CD64 ANTIGEN; LIGAND; MICRORNA; MICRORNA 125A 5P; MICRORNA 125B; MICRORNA 146A; MICRORNA 146B 5P; MICRORNA 150; MICRORNA 191 ISO; MICRORNA 223; MICRORNA 3173 3P; MICRORNA 342 3P; MICRORNA 4772 3P; MICRORNA 4772 5P; MICRORNA 4772 5P ISO; TOLL LIKE RECEPTOR; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; CELL LEVEL; CLINICAL ARTICLE; COHORT ANALYSIS; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; FEMALE; GENETIC SCREENING; GENOME ANALYSIS; HUMAN; INTENSIVE CARE UNIT; MALE; MONOCYTE; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RECEIVER OPERATING CHARACTERISTIC; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; SEPSIS; SEQUENCE ANALYSIS; SWEDEN; SYSTEMIC INFLAMMATORY RESPONSE SYNDROME; UNITED KINGDOM; VALIDATION STUDY;

ADULT; BIOLOGICAL MARKERS; COHORT STUDIES; FEMALE; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTENSIVE CARE UNITS; LINEAR MODELS; MALE; MICRORNAS; MIDDLE AGED; MONOCYTES; PROGNOSIS; REAL-TIME POLYMERASE CHAIN REACTION; SEPSIS; TRANSCRIPTOME;

EID: 84885790547     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0075918     Document Type: Article

References (41)

1. Angus DC, Linde-Zwirble WT, Lidicker J, Clermont G, Carcillo J, et al. (2001) Epidemiology of severe sepsis in the United States: analysis of incidence, outcome, and associated costs of care. Crit Care Med 29: 1303-1310.
2. Dellinger RP, Carlet JM, Masur H, Gerlach H, Calandra T, et al. (2004) Surviving Sepsis Campaign guidelines for management of severe sepsis and septic shock. Crit Care Med 32: 858-873.
3. Gaieski DF, Pines JM, Band RA, Mikkelsen ME, Massone R, et al. (2009) Impact of time to antibiotics on survival in patients with severe sepsis or septic shock in whom early goal-directed therapy was initiated in the emergency department. Crit Care Med.
4. Levy MM, Dellinger RP, Townsend SR, Linde-Zwirble WT, Marshall JC, et al. (2010) The Surviving Sepsis Campaign: results of an international guideline-based performance improvement program targeting severe sepsis. Intensive Care Med 36: 222-231.
5. Beale R, Reinhart K, Brunkhorst FM, Dobb G, Levy M, et al. (2009) Promoting Global Research Excellence in Severe Sepsis (PROGRESS): lessons from an international sepsis registry. Infection 37: 222-232.
6. Baltimore D, Boldin MP, O'Connell RM, Rao DS, Taganov KD, (2008) MicroRNAs: new regulators of immune cell development and function. Nat Immunol 9: 839-845.
7. O'Connell RM, Chaudhuri AA, Rao DS, Gibson WS, Balazs AB, et al. (2010) MicroRNAs enriched in hematopoietic stem cells differentially regulate long-term hematopoietic output. Proc Natl Acad Sci U S A 107: 14235-14240.
8. Calin GA, Croce CM, (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6: 857-866.
9. Ji J, Shi J, Budhu A, Yu Z, Forgues M, et al. (2009) MicroRNA expression, survival, and response to interferon in liver cancer. N Engl J Med 361: 1437-1447.
10. Vasilescu C, Rossi S, Shimizu M, Tudor S, Veronese A, et al. (2009) MicroRNA fingerprints identify miR-150 as a plasma prognostic marker in patients with sepsis. PLoS One 4: e7405.
11. Marcucci G, Radmacher MD, Maharry K, Mrozek K, Ruppert AS, et al. (2008) MicroRNA expression in cytogenetically normal acute myeloid leukemia. N Engl J Med 358: 1919-1928.
12. O'Connell RM, Taganov KD, Boldin MP, Cheng G, Baltimore D, (2007) MicroRNA-155 is induced during the macrophage inflammatory response. Proc Natl Acad Sci U S A 104: 1604-1609.
13. Tili E, Michaille JJ, Cimino A, Costinean S, Dumitru CD, et al. (2007) Modulation of miR-155 and miR-125b levels following lipopolysaccharide/TNF-alpha stimulation and their possible roles in regulating the response to endotoxin shock. J Immunol 179: 5082-5089.
14. Wang JF, Yu ML, Yu G, Bian JJ, Deng XM, et al. (2010) Serum miR-146a and miR-223 as potential new biomarkers for sepsis. Biochem Biophys Res Commun 394: 184-188.
15. Delfour O VD, Atzorn V, Michot B (2007) The passionate race for microARN detection and function deciphering." Clarke, N.J and Sanseau, P(eds): "microARN: Biology, Function and Expression. DNA Press Chapter 5: 38.
16. Dyson A, Singer M, (2009) Animal models of sepsis: why does preclinical efficacy fail to translate to the clinical setting? Crit Care Med 37: S30-37.
17. Deitch EA, (2005) Rodent models of intra-abdominal infection. Shock 24 Suppl 1: 19-23.
18. Levy MM, Fink MP, Marshall JC, Abraham E, Angus D, et al. (2003) 2001 SCCM/ESICM/ACCP/ATS/SIS International Sepsis Definitions Conference. Crit Care Med 31: 1250-1256.
19. Josefson P, Stralin K, Ohlin A, Ennefors T, Dragsten B, et al. (2011) Evaluation of a commercial multiplex PCR test (SeptiFast) in the etiological diagnosis of community-onset bloodstream infections. Eur J Clin Microbiol Infect Dis 30: 1127-1134.
20. Invitrogen Website, TRIzol Reagent and TRIzol LS Reagent (2011) Available: http://tools.invitrogen.com/Content/SFS/ProductNotes/F_071215_Trizol%20and%20Trizol%20LS.pdf. Accessed 2013 Aug 27.
21. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18: 610-621.
22. Meyer SU, Pfaffl MW, Ulbrich SE, (2010) Normalization strategies for microRNA profiling experiments: a 'normal' way to a hidden layer of complexity? Biotechnol Lett 32: 1777-1788.
23. Jenner RG, Townsend MJ, Jackson I, Sun K, Bouwman RD, et al. (2009) The transcription factors T-bet and GATA-3 control alternative pathways of T-cell differentiation through a shared set of target genes. Proc Natl Acad Sci U S A 106: 17876-17881.
24. Taganov KD, Boldin MP, Chang KJ, Baltimore D, (2006) NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci U S A 103: 12481-12486.
25. Carrigan SD, Scott G, Tabrizian M, (2004) Toward resolving the challenges of sepsis diagnosis. Clin Chem 50: 1301-1314.
26. Ivady B, Beres BJ, Szabo D, (2011) Recent advances in sepsis research: novel biomarkers and therapeutic targets. Curr Med Chem 18: 3211-3225.
27. Simms HH, Frank MM, Quinn TC, Holland S, Gaither TA, (1989) Studies on phagocytosis in patients with acute bacterial infections. J Clin Invest 83: 252-260.
28. Cid J, Aguinaco R, Sanchez R, Garcia-Pardo G, Llorente A, (2010) Neutrophil CD64 expression as marker of bacterial infection: a systematic review and meta-analysis. J Infect 60: 313-319.
29. Ruan K, Fang X, Ouyang G, (2009) MicroRNAs: novel regulators in the hallmarks of human cancer. Cancer Lett 285: 116-126.
30. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
31. Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
32. Wang QZ, Xu W, Habib N, Xu R, (2009) Potential uses of microRNA in lung cancer diagnosis, prognosis, and therapy. Curr Cancer Drug Targets 9: 572-594.
33. Wang H, Zhang P, Chen W, Feng D, Jia Y, et al. (2012) Serum microRNA signatures identified by Solexa sequencing predict sepsis patients' mortality: a prospective observational study. PLoS One 7: e38885.
34. Sun X, Icli B, Wara AK, Belkin N, He S, et al. (2012) MicroRNA-181b regulates NF-kappaB-mediated vascular inflammation. J Clin Invest 122: 1973-1990.
35. Vaz C, Ahmad HM, Sharma P, Gupta R, Kumar L, et al. (2010) Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics 11: 288.
36. Schotte D, Moqadam FA, Lange-Turenhout EA, Chen C, van Ijcken WF, et al. (2011) Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia. Leukemia 25: 1389-1399.
37. Ugras S, Brill E, Jacobsen A, Hafner M, Socci ND, et al. (2011) Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. Cancer Res 71: 5659-5669.
38. Han Y, Chen J, Zhao X, Liang C, Wang Y, et al. (2011) MicroRNA expression signatures of bladder cancer revealed by deep sequencing. PLoS One 6: e18286.
39. Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, et al. (2010) Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. Blood 116: e118-127.
40. Pritchard CC, Kroh E, Wood B, Arroyo JD, Dougherty KJ, et al. (2012) Blood cell origin of circulating microRNAs: a cautionary note for cancer biomarker studies. Cancer Prev Res (Phila) 5: 492-497.
41. Standage SW, Wong HR, (2011) Biomarkers for pediatric sepsis and septic shock. Expert Rev Anti Infect Ther 9: 71-79.