Classification of patients with sepsis according to blood genomic endotype: a prospective cohort study

The Lancet Respiratory Medicine

Volumn 5, Issue 10, 2017, Pages 816-826

  Scicluna, Brendon P ^a   van Vught, Lonneke A ^a   Zwinderman, Aeilko H ^a   Wiewel, Maryse A ^a   Davenport, Emma E ^b   Burnham, Katie L ^b   Nürnberg, Peter ^c,d   Schultz, Marcus J ^a   Horn, Janneke ^a   Cremer, Olaf L ^e   Bonten, Marc J ^e   Hinds, Charles J ^f   Wong, Hector R ^g,h   Knight, Julian C ^b   van der Poll, Tom ^a   de Beer, Friso M ⁱ   Bos, Lieuwe D J ⁱ   Frencken, Jos F ⁱ   Koster Brouwer, Maria E ⁱ   van de Groep, Kirsten ⁱ   Verboom, Diana M ⁱ   Glas, Gerie J ⁱ   van Hooijdonk, Roosmarijn T M ⁱ   Hoogendijk, Arie J ⁱ   Huson, Mischa A ⁱ   Klouwenberg, Peter M Klein ⁱ   Ong, David S Y ⁱ   Schouten, Laura R A ⁱ   Straat, Marleen ⁱ   Witteveen, Esther ⁱ   Wieske, Luuk ⁱ   more..

^a ACADEMIC MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF COLOGNE   (Germany)

^d UNIVERSITY OF COLOGNE   (Germany)

^e UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^f QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^g CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^h UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

ⁱ NONE

Author keywords

[No Author keywords available]

Indexed keywords

BISPHOSPHOGLYCERATE MUTASE; TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1;

ADULT; APACHE; ARTICLE; BPGM GENE; CARDIOVASCULAR DISEASE; CHARLSON COMORBIDITY INDEX; CHRONIC OBSTRUCTIVE LUNG DISEASE; CLINICAL PRACTICE; COHORT ANALYSIS; COMMUNITY ACQUIRED PNEUMONIA; COMORBIDITY; CONSENSUS DEVELOPMENT; CONTROLLED STUDY; DIABETES MELLITUS; FEMALE; GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; HAZARD RATIO; HOSPITAL ADMISSION; HUMAN; HYPERTENSION; INTENSIVE CARE UNIT; KIDNEY FAILURE; MACHINE LEARNING; MAJOR CLINICAL STUDY; MALE; MALIGNANT NEOPLASM; MORTALITY; NETHERLANDS; OBSERVATIONAL STUDY; PATIENT CODING; PATIENT SELECTION; PERSONALIZED MEDICINE; PREDICTION; PRIORITY JOURNAL; PROSPECTIVE STUDY; RELIABILITY; RESPIRATORY FAILURE; RISK ASSESSMENT; SEPSIS; SEQUENTIAL ORGAN FAILURE ASSESSMENT SCORE; SURVIVAL RATE; TAP2 GENE; UNITED KINGDOM; AGED; CLASSIFICATION; CLINICAL TRIAL; COMMUNITY ACQUIRED INFECTION; COMPLICATION; GENETIC MARKER; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; MIDDLE AGED; MULTICENTER STUDY; PHENOTYPE; PNEUMONIA; PROCEDURES; STATISTICS AND NUMERICAL DATA;

AGED; COMMUNITY-ACQUIRED INFECTIONS; FEMALE; GENE EXPRESSION PROFILING; GENETIC MARKERS; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; INTENSIVE CARE UNITS; MALE; MIDDLE AGED; PHENOTYPE; PNEUMONIA; PROSPECTIVE STUDIES; SEPSIS;

EID: 85028540198     PISSN: 22132600     EISSN: 22132619     Source Type: Journal    
DOI: 10.1016/S2213-2600(17)30294-1     Document Type: Article

References (42)

1. Angus, DC, van der Poll, T, Severe sepsis and septic shock. N Engl J Med 369 (2013), 840–851.
2. Liu, V, Escobar, GJ, Greene, JD, et al. Hospital deaths in patients with sepsis from 2 independent cohorts. JAMA 312 (2014), 90–92.
3. Cohen, J, Vincent, JL, Adhikari, NK, et al. Sepsis: a roadmap for future research. Lancet Infect Dis 15 (2015), 581–614.
4. Maslove, DM, Wong, HR, Gene expression profiling in sepsis: timing, tissue, and translational considerations. Trends Mol Med 20 (2014), 204–213.
5. Scicluna, BP, Klein Klouwenberg, PM, van Vught, LA, et al. A molecular biomarker to diagnose community-acquired pneumonia on intensive care unit admission. Am J Respir Crit Care Med 192 (2015), 826–835.
6. McHugh, L, Seldon, TA, Brandon, RA, et al. 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, 2015, e1001916.
7. Sweeney, TE, Shidham, A, Wong, HR, Khatri, P, A comprehensive time-course-based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set. Sci Transl Med, 7, 2015, 287ra71.
8. Parlato, M, Cavaillon, JM, Host response biomarkers in the diagnosis of sepsis: a general overview. Methods Mol Biol 1237 (2015), 149–211.
9. Sweeney, TE, Wong, HR, Risk stratification and prognosis in sepsis: what have we learned from microarrays?. Clin Chest Med 37 (2016), 209–218.
10. Curtis, C, Shah, SP, Chin, SF, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486 (2012), 346–352.
11. Guinney, J, Dienstmann, R, Wang, X, et al. The consensus molecular subtypes of colorectal cancer. Nat Med 21 (2015), 1350–1356.
12. Klein Klouwenberg, PM, Ong, DSY, Bos, LDJ, et al. Interobserver agreement of centers for disease control and prevention criteria for classifying infections in critically ill patients. Crit Care Med 41 (2013), 2373–2378.
13. van Vught, LA, Klein Klouwenberg, PM, Spitoni, C, et al. Incidence, risk factors, and attributable mortality of secondary infections in the intensive care unit after admission for sepsis. JAMA 315 (2016), 1469–1479.
14. Garner, JS, Jarvis, WR, Emori, TG, Horan, TC, Hughes, JM, CDC definitions for nosocomial infections, 1988. Am J Infect Control 16 (1988), 128–140.
15. Calandra, T, Cohen, J, The international sepsis forum consensus conference on definitions of infection in the intensive care unit. Crit Care Med 33 (2005), 1538–1548.
16. Levy, MM, Fink, MP, Marshall, JC, et al. 2001 SCCM/ESICM/ACCP/ATS/SIS international sepsis definitions conference. Crit Care Med 31 (2003), 1250–1256.
17. Davenport, EE, Burnham, KL, Radhakrishnan, J, et al. Genomic landscape of the individual host response and outcomes in sepsis: a prospective cohort study. Lancet Respir Med 4 (2016), 259–271.
18. Wong, HR, Cvijanovich, N, Allen, GL, et al. Genomic expression profiling across the pediatric systemic inflammatory response syndrome, sepsis, and septic shock spectrum. Crit Care Med 37 (2009), 1558–1566.
19. Verhaak, RG, Hoadley, KA, Purdom, E, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17 (2010), 98–110.
20. Wilkerson, MD, Hayes, DN, ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics 26 (2010), 1572–1573.
21. De Sousa, E, Melo, F, Wang, X, Jansen, M, et al. Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions. Nat Med 19 (2013), 614–618.
22. Rousseeuw, PJ, Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. Comput Appl Math 20 (1987), 53–65.
23. Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K. Cluster: cluster analysis basics and extensions. R package, version 1153. 2014.
24. Brunet, JP, Tamayo, P, Golub, TR, Mesirov, JP, Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci USA 101 (2004), 4164–4169.
25. Breiman, L, Random forests. Machine Learning 45 (2001), 5–32.
26. Slawski, M, Daumer, M, Boulesteix, AL, CMA: a comprehensive Bioconductor package for supervised classification with high dimensional data. BMC Bioinformatics, 9, 2008, 439.
27. Kundu, S, Aulchenko, YS, van Duijn, CM, Janssens, AC, PredictABEL: an R package for the assessment of risk prediction models. Eur J Epidemiol 26 (2011), 261–264.
28. Zimmerman, JE, Kramer, AA, McNair, DS, Malila, FM, Acute Physiology and Chronic Health Evaluation (APACHE) IV: hospital mortality assessment for today's critically ill patients. Crit Care Med 34 (2006), 1297–1310.
29. Vincent, JL, Moreno, R, Takala, J, et al. The SOFA (Sepsis-related Organ Failure Assessment) score to describe organ dysfunction/failure. Intensive Care Med 22 (1996), 707–710.
30. Pencina, MJ, D'Agos'ino, RB Sr, D'Agostino, RB Jr, Vasan, RS, Evaluating the added predictive ability of a new marker: from area under the ROC curve to reclassification and beyond. Stat Med 27 (2008), 157–172 discussion 207–12.
31. Pollack, MM, Ruttimann, UE, Getson, PR, Pediatric risk of mortality (PRISM) score. Crit Care Med 16 (1988), 1110–1116.
32. Rosa, R, Blouquit, Y, Calvin, MC, Prome, D, Prome, JC, Rosa, J, Isolation, characterization, and structure of a mutant 89 Arg— Cys bisphosphoglycerate mutase. Implication of the active site in the mutation. J Biol Chem 264 (1989), 7837–7843.
33. Kelly, A, Powis, SH, Kerr, LA, et al. Assembly and function of the two ABC transporter proteins encoded in the human major histocompatibility complex. Nature 355 (1992), 641–644.
34. Maslove, DM, Tang, BM, McLean, AS, Identification of sepsis subtypes in critically ill adults using gene expression profiling. Crit Care, 16, 2012, R183.
35. Wheeler, DS, Wong, HR, Zingarelli, B, Pediatric sepsis—part I: “Children are not small adults!”. Open Inflamm J 4 (2011), 4–15.
36. PrabhuDas, M, Adkins, B, Gans, H, et al. Challenges in infant immunity: implications for responses to infection and vaccines. Nat Immunol 12 (2011), 189–194.
37. Amelio, I, Cutruzzola, F, Antonov, A, Agostini, M, Melino, G, Serine and glycine metabolism in cancer. Trends Biochemical Sci 39 (2014), 191–198.
38. Cheng, SC, Scicluna, BP, Arts, RJ, et al. Broad defects in the energy metabolism of leukocytes underlie immunoparalysis in sepsis. Nat Immunol 17 (2016), 406–413.
39. Hotchkiss, RS, Monneret, G, Payen, D, Sepsis-induced immunosuppression: from cellular dysfunctions to immunotherapy. Nat Rev Immunol 13 (2013), 862–874.
40. Marshall, JC, Why have clinical trials in sepsis failed?. Trends Mol Med 20 (2014), 195–203.
41. Angus, DC, The search for effective therapy for sepsis: back to the drawing board?. JAMA 306 (2011), 2614–2615.
42. van der Poll, T, Future of sepsis therapies. Crit Care, 20, 2016, 106.