US20170073734A1 - Diagnostic for Sepsis - Google Patents

Diagnostic for Sepsis Download PDF

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US20170073734A1
US20170073734A1 US15/124,333 US201515124333A US2017073734A1 US 20170073734 A1 US20170073734 A1 US 20170073734A1 US 201515124333 A US201515124333 A US 201515124333A US 2017073734 A1 US2017073734 A1 US 2017073734A1
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genes
expression
gene signature
sepsis
difference
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Robert E. W. Hancock
Olga M. Pena Serrato
David G. Hancock
John Boyd
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    • C12N15/1068—Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/172—Haplotypes

Definitions

  • the present invention relates to the field of diagnostics and, in particular, to a unique set of DNA sequences that in combination enable the early diagnosis of sepsis, and the prediction of severe sepsis and/or organ failure.
  • Bacterial endotoxins are potent inducers of inflammation and have been suggested as triggers for sepsis, as the cause of an early life-threatening cytokine storm and septic shock [Opal S M. Contributions to Nephrology 2010; 167: 14-24; Salomao R, et al. Shock 2012; 38:227-42].
  • LPS can also generate an opposite effect known as endotoxin tolerance, defined as the severely reduced capacity of the cell to respond to LPS and other bacterial products during a second exposure to the stimulus [Otto G P, et al. Critical Care 2011; 15:R183].
  • endotoxin tolerance also termed cellular reprogramming since it can be induced by other microbial molecules, is not an anti-inflammatory state of cells but rather a reprogramming of cells so they are no longer able of responding to multiple microbial signatures, including endotoxin.
  • endotoxin tolerance may be associated with the immunosuppressive state that has been primarily observed during late-stage severe sepsis [Otto G P, et al. 2011; Cavaillon J, et al. J Endotoxin Res 2005; 11(5): 311-20; Cavaillon J, Adib-Conquy M. Critical Care Medicine 2006; 10:233].
  • this relationship remains poorly characterized, in part due to the limitations of the ex vivo cytokine assays employed to date.
  • the clinical dogma is to identify and treat sepsis, especially in its early stages, as an excessive inflammatory response.
  • Biomarkers for the diagnosis of sepsis have been proposed in U.S. Pat. No. 7,767,395; U.S. Patent Application Publication No. 2011/0312521; U.S. Patent Application Publication No. 2011/0076685; International Patent Application Publication No. WO 2014/209238, and International Patent Application Publication No. WO 2013/152047.
  • the present invention relates generally to a diagnostic for early severe sepsis.
  • the invention relates to a method for diagnosing sepsis in a subject, comprising determining in a biological sample obtained from the subject a level of expression for each of a plurality of Endotoxin Tolerance Signature genes to provide a sample gene signature, and comparing the sample gene signature with a reference gene signature, wherein the reference gene signature represents a standard level of expression of each of the plurality of genes; wherein a difference between the sample gene signature and the reference gene signature indicates that the subject has sepsis.
  • the invention in another aspect, relates to a method for identifying a subject at risk of developing severe sepsis, comprising determining in a biological sample obtained from the subject a level of expression for each of a plurality of Endotoxin Tolerance Signature genes to provide a sample gene signature, and comparing the sample gene signature with a reference gene signature, wherein the reference gene signature represents a standard level of expression of each of the plurality of genes; wherein a difference between the sample gene signature and the reference gene signature indicates that the subject is at risk of developing severe sepsis.
  • the invention in another aspect, relates to a method for identifying a subject at risk of organ failure, comprising determining in a biological sample obtained from the subject a level of expression for each of a plurality of Endotoxin Tolerance Signature genes to provide a sample gene signature, and comparing the sample gene signature with a reference gene signature, wherein the reference gene signature represents a standard level of expression of each of the plurality of genes; wherein a difference between the sample gene signature and the reference gene signature indicates that the subject is at risk of organ failure.
  • the plurality of genes is selected from ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2, EMR1, EMR3, FBP1, FCER1G, FCER2, FPR1, FPR2, GK, GPNMB, GPR137B, HBEGF, HIST1H1C, HIST2H2AA3, HIST2H2AC, HK2, HK3, HPSE, HSD11B1, HTRA1, IL18BP, IL3RA, ITGB8, KIAA1199, LILRA3, LILRA5, LIPA, LY86, MARCO, MGST1, MMP7, MT1
  • the plurality of genes is selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes comprises C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes consists of C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the invention relates to a method for diagnosing endotoxin tolerance in a subject, the method comprising: a) determining in a biological sample obtained from the subject a level of expression for each of a plurality of genes selected from ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2, EMR1, EMR3, FBP1, FCER1G, FCER2, FPR1, FPR2, GK, GPNMB, GPR137B, HBEGF, HIST1H1C, HIST2H2AA3, HIST2H2AC, HK2, HK3, HPSE, HSD11B1, HTRA1,
  • the plurality of genes is selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes comprises C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes consists of C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the invention in another aspect, relates to a method for treating sepsis comprising administering an effective amount of one or more antibiotics to a subject who has been diagnosed as having sepsis by the method described above.
  • the invention in another aspect, relates to a method for treating sepsis in a subject, the method comprising: a) determining whether the subject has sepsis or is at risk of developing sepsis by: (i) determining in a biological sample obtained from the subject a level of expression for each of a plurality of genes selected from ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2, EMR1, EMR3, FBP1, FCER1G, FCER2, FPR1, FPR2, GK, GPNMB, GPR137B, HBEGF, HIST1H1C, HIST2H2AA3, HIST
  • the plurality of genes is selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, REIN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes comprises C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, REIN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes consists of C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, REIN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the invention in another aspect, relates to a method for decreasing the risk of organ failure in a subject comprising administering an effective amount of one or more antibiotics to a subject who has been diagnosed as having sepsis or being at risk of developing sepsis by the method described above.
  • the invention in another aspect, relates to a method for decreasing the risk of organ failure in a subject, the method comprising: a) determining whether the subject is at risk of organ failure by: (i) determining in a biological sample obtained from the subject a level of expression for each of a plurality of genes selected from ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2, EMR1, EMR3, FBP1, FCER1G, FCER2, FPR1, FPR2, GK, GPNMB, GPR137B, HBEGF, HIST1H1C, HIST2H2AA3, HIST2H2AC, HK2,
  • the plurality of genes is selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes comprises C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes consists of C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the invention in another aspect, relates to a method for decreasing the risk of a subject developing severe sepsis comprising administering an effective amount of an agent that counteracts endotoxin tolerance to a subject who has been diagnosed as being at risk of developing severe sepsis by the method described above.
  • the invention in another aspect, relates to a method for decreasing the risk of organ failure in a subject comprising administering an effective amount of an agent that counteracts endotoxin tolerance to a subject who has been diagnosed as being at risk of organ failure by the method described above.
  • the invention in another aspect, relates to a method for decreasing the risk of a subject developing severe sepsis or organ failure comprising administering to the subject an effective amount of an agent that counteracts endotoxin tolerance.
  • the method may further comprise determining that the subject is at risk of developing severe sepsis or organ failure by: (a) determining in a biological sample obtained from the subject the level of expression of a plurality of genes selected from ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2, EMR1, EMR3, FBP1, FCER1G, FCER2, FPR1, FPR2, GK, GPNMB
  • the plurality of genes is selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes comprises C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes consists of C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the invention in another aspect, relates to a method for identifying a candidate agent for the treatment of sepsis, the method comprising: a) contacting an endotoxin tolerant cell with a test agent, b) determining the level of expression for each of a plurality of Endotoxin Tolerance Signature genes in the endotoxin tolerant cell to provide an expression signature, c) comparing the expression signature with a reference expression signature, wherein the reference signature represents the levels of expression of the plurality of genes in a normal cell, and d) selecting the test agent as a candidate agent for treatment of sepsis when the expression signature substantially corresponds with the reference signature.
  • the plurality of genes is selected from ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2, EMR1, EMR3, FBP1, FCER1G, FCER2, FPR1, FPR2, GK, GPNMB, GPR137B, HBEGF, HIST1H1C, HIST2H2AA3, HIST2H2AC, HK2, HK3, HPSE, HSD11B1, HTRA1, IL18BP, IL3RA, ITGB8, KIAA1199, LILRA3, LILRA5, LIPA, LY86, MARCO, MGST1, MMP7, MT1
  • the plurality of genes is selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes comprises C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes consists of C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the invention relates to a kit for determining a level of expression for each of a plurality of genes selected from ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2, EMR1, EMR3, FBP1, FCER1G, FCER2, FPR1, FPR2, GK, GPNMB, GPR137B, HBEGF, HIST1H1C, HIST2H2AA3, HIST2H2AC, HK2, HK3, HPSE, HSD11B1, HTRA1, IL18BP, IL3RA, ITGB8, KIAA1199, LILRA3, LILRA5, LIPA,
  • the plurality of genes is selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes comprises C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes consists of C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the invention in another aspect, relates to a microarray for detecting expression of a plurality of Endotoxin Tolerance Signature genes in a sample, the microarray comprising a plurality of polynucleotide probes attached to a solid support, each of the polynucleotide probes capable of specifically hybridizing to an expression product of a respective one of the plurality of genes or complement thereof.
  • the plurality of genes are selected from ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2, EMR1, EMR3, FBP1, FCER1G, FCER2, FPR1, FPR2, GK, GPNMB, GPR137B, HBEGF, HIST1H1C, HIST2H2AA3, HIST2H2AC, HK2, HK3, HPSE, HSD11B1, HTRA1, IL18BP, IL3RA, ITGB8, KIAA1199, LILRA3, LILRA5, LIPA, LY86, MARCO, MGST1, MMP7, MT1
  • the plurality of genes is selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes comprises C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of genes consists of C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • FIG. 1 shows a schematic representation of the method used to define the Endotoxin Tolerance Signature and the Inflammatory Signature.
  • the Endotoxin Tolerance Signature was defined as 99 genes uniquely differentially expressed in endotoxin-tolerant PBMCs, but not inflammatory PBMCs, as compared to controls (fold change>2, p-value ⁇ 0.05).
  • the Inflammatory Signature was defined as a 93 gene signature by selecting genes that were consistently differentially expressed in an in vivo endotoxaemia dataset.
  • FIG. 2 demonstrates that reanalysis of differential gene expression from sepsis patients from published datasets showed a strong association with the Endotoxin Tolerance Signature.
  • a gene-set test approach ROAST, was used to characterize the enrichment of “Endotoxin Tolerance” in sepsis patients versus controls from 9 previously published datasets. All datasets contained sepsis patients recruited at day 1 or 3 post-ICU admission and were compared to “healthy” controls.
  • the ROAST gene-set test was run with 99999 rotations so the most significant p-value resulting from this test is 0.00001.
  • P-values from the ROAST gene-set test were graphed as log (1/p-value), but the untransformed p-values are shown for ease of visualization.
  • FIG. 3 shows that sepsis patients based on published datasets generally showed a less significant association with the Inflammatory Signature.
  • a gene-set test approach, ROAST was used to characterize the enrichment of Inflammatory signature (white) relative to the Endotoxin Tolerance Signature (grey) in sepsis patients cf. controls in 9 previously published datasets. All datasets contained sepsis patients recruited at days 1 and/or 3 post-ICU admission and were compared to ‘healthy’ controls.
  • the ROAST gene-set test was run with 99999 rotations so the most significant p-value resulting from this test is 0.00001.
  • P-values from the ROAST gene-set test were graphed as log (1/p-value), but the untransformed p-values are shown for ease of visualization.
  • FIG. 4 reveals that the association between endotoxin tolerance and sepsis is independent of the specific method used to define the Endotoxin Tolerance Signature.
  • Different endotoxin tolerance related-signatures were identified based on genes uniquely differentially expressed in endotoxin-tolerant PBMCs, but not inflammatory PBMCs, as compared to controls at various fold-change (FC) and P-value cut-offs. Datasets were as described in the legend to FIG. 3 except the Day 0 RNA-Seq dataset is the one described here.
  • the final Endotoxin Tolerance Signature was defined at fold-change (FC) and P-value cut-offs of 2 and 0.05, respectively.
  • FIG. 5 shows that the Endotoxin Tolerance Signature is strongly associated with sepsis patients at first clinical presentation.
  • a gene-set test approach was used to characterize the enrichment, cf. controls, of the Endotoxin Tolerance and Inflammatory signatures in prospective sepsis patients from a unique in-house cohort recruited on first clinical suspicion of sepsis (i.e. generally in the emergency ward prior to ICU admission).
  • Patients groups were subsequently defined based on retrospective clinical characteristics as ‘Sepsis’ or ‘No Sepsis’ consistent with the current sepsis criteria (Table 3). Analyses were performed comparing ‘sepsis’ and ‘no sepsis’ group vs. controls (a) and ‘sepsis’ vs. ‘no sepsis’ group (b). Additionally, enrichment of the signature was also analyzed based on microbial culture results within the ‘Sepsis’ group (c) and the ‘No Sepsis’ (d) group (c
  • FIG. 6 shows that the Endotoxin Tolerance Signature is strongly associated with sepsis patients at first clinical presentation and is associated with the severity of the disease and organ failure.
  • a gene-set test approach was used to characterize the enrichment, cf. surgical controls, of the Endotoxin Tolerance and Inflammatory signatures in prospective sepsis patients as described for FIG. 5 .
  • FIG. 7 shows a core set of endotoxin tolerance genes characteristic of sepsis patients.
  • a core set of 31 of the 99 genes from the Endotoxin Tolerance Signature was determined based on the most frequently differentially expressed genes observed in all sepsis patient studies (literature and in-house datasets). For better visual comparison across different studies, each individual dataset was further transformed by dividing gene expression values into six equal bins. Data is presented as a heatmap with lightest and darkest shading representing relatively large and relatively small changes in expression, respectively. The differentiation was more obvious as a color heatmap.
  • FIG. 8 demonstrates a sub-network of genes from the Endotoxin Tolerance Signature identified using the j-Activemodules plug-in of Cytoscape.
  • First a network was created by including first level interactors of the genes listed in Table 1 and then subjected to analysis using j-Activemodules which identifies particularly dense (i.e. highly interconnected) subnetworks. Dark nodes (genes) are highly dysregulated, and light nodes are direct interactors of the dysregulated genes, lines represent “edges” and indicate experimentally proven interactions.
  • the fact that 60 of the 99 genes in the signature were tightly interconnected in the human cell implicates a biologically meaningful relationship between these genes; i.e.
  • Endotoxin Tolerance Signature A unique gene signature characteristic of endotoxin tolerance (an “Endotoxin Tolerance Signature”) is identified herein that may be used in the diagnosis of sepsis.
  • Endotoxin Tolerance Signature is able to differentiate between suspected sepsis patients who either did or did not go on to develop sepsis, and also to predict organ failure.
  • Certain embodiments of the invention thus relate to methods of diagnosing endotoxin tolerance in a subject, for example a patient known or suspected of having sepsis, using the Endotoxin Tolerance Signature described herein.
  • the presence of endotoxin tolerance is shown to be an indication that a patient has sepsis, and is furthermore an indication that the patient is at risk of developing severe sepsis and/or organ failure.
  • Certain embodiments of the invention relate to methods of diagnosing sepsis in a subject using the Endotoxin Tolerance Signature described herein.
  • the sepsis is severe sepsis.
  • Certain embodiments relate to methods of confirming sepsis in a subject suspected of having sepsis a subject using the Endotoxin Tolerance Signature described herein. Some embodiments relate to methods of predicting whether a subject is at risk of developing severe sepsis and/or organ failure using the Endotoxin Tolerance Signature described herein.
  • endotoxin tolerance-mediated immune dysfunction has been determined to be present in a predominant manner upon first presentation and throughout the clinical course of disease.
  • the data provided herein re-defines sepsis as a disease characterized by endotoxin tolerance-mediated immune dysfunction at all stages of clinical disease, and thus identifies endotoxin tolerance as a potential therapeutic target in early and late sepsis.
  • Certain embodiments of the invention thus relate to methods of treating patients identified as having endotoxin tolerance, for example by using the diagnostic methods described herein, in order to reduce the risk that they will develop sepsis, severe sepsis and/or organ failure. Certain embodiments relate to methods of treating patients having sepsis, including severe sepsis, with an agent that counteracts endotoxin tolerance.
  • Certain embodiments of the invention relate to methods of identifying candidate agents for treatment of sepsis using the Endotoxin Tolerance Signature described herein.
  • Certain embodiments relate to a method for diagnosing sepsis in a subject, comprising determining in a biological sample obtained from the subject a level of expression for each of a plurality of Endotoxin Tolerance Signature genes to provide a sample gene signature, and comparing the sample gene signature with a reference gene signature, wherein the reference gene signature represents a standard level of expression of each of the plurality of genes; wherein a difference between the sample gene signature and the reference gene signature indicates that the subject has sepsis.
  • Certain embodiments relate to a method for identifying a subject at risk of developing severe sepsis, comprising determining in a biological sample obtained from the subject a level of expression for each of a plurality of Endotoxin Tolerance Signature genes to provide a sample gene signature, and comparing the sample gene signature with a reference gene signature, wherein the reference gene signature represents a standard level of expression of each of the plurality of genes; wherein a difference between the sample gene signature and the reference gene signature indicates that the subject is at risk of developing severe sepsis.
  • Certain embodiments relate to a method for identifying a subject at risk of organ failure, comprising determining in a biological sample obtained from the subject a level of expression for each of a plurality of Endotoxin Tolerance Signature genes to provide a sample gene signature, and comparing the sample gene signature with a reference gene signature, wherein the reference gene signature represents a standard level of expression of each of the plurality of genes; wherein a difference between the sample gene signature and the reference gene signature indicates that the subject is at risk of organ failure.
  • plurality means more than one, for example, two or more, three or more, four or more, and the like.
  • gene refers to a nucleic acid sequence that comprises coding sequences necessary for producing a polypeptide or precursor. Control sequences that direct and/or control expression of the coding sequences may also be encompassed by the term “gene” in some instances.
  • the polypeptide or precursor may be encoded by a full length coding sequence or by a portion of the coding sequence.
  • a gene may contain one or more modifications in either the coding or the untranslated regions that could affect the biological activity or the chemical structure of the polypeptide or precursor, the rate of expression, or the manner of expression control.
  • Such modifications include, but are not limited to, mutations, insertions, deletions, and substitutions of one or more nucleotides, including single nucleotide polymorphisms that occur naturally in the population.
  • the gene may constitute an uninterrupted coding sequence or it may include one or more subsequences.
  • the term “gene” as used herein includes variants of the genes identified in Table 1.
  • gene expression profile or “gene signature” refer to a group of genes expressed by a particular cell or tissue type wherein expression of the genes taken together, or the differential expression of such genes, is indicative and/or predictive of a certain condition, such as sepsis.
  • nucleic acid refers to a molecule comprised of one or more nucleotides, for example, ribonucleotides, deoxyribonucleotides, or both.
  • the term includes monomers and polymers of nucleotides, with the nucleotides being bound together, in the case of the polymers, in sequence, typically via 5′ to 3′ linkages, although alternative linkages are also contemplated in some embodiments.
  • the nucleotide polymers may be single or double-stranded.
  • the nucleotides may be naturally occurring or may be synthetically produced analogs that are capable of forming base-pair relationships with naturally occurring base pairs.
  • non-naturally occurring bases that are capable of forming base-pairing relationships include, but are not limited to, aza and deaza pyrimidine analogs, aza and deaza purine analogs, and other heterocyclic base analogs, wherein one or more of the carbon and nitrogen atoms of the pyrimidine rings have been substituted by heteroatoms, e.g., oxygen, sulphur, selenium, phosphorus, and the like.
  • heteroatoms e.g., oxygen, sulphur, selenium, phosphorus, and the like.
  • nucleic acid sequence “TATAC” corresponds to a reference sequence “TATAC” and is complementary to a reference sequence “GTATA.”
  • complement thereof means a nucleic acid that is complementary in nucleotide sequence to a referenced nucleic acid.
  • the complement of an mRNA may be an RNA polynucleotide sequence or a DNA polynucleotide sequence.
  • the complement of a DNA polynucleotide may be an RNA polynucleotide or a DNA polynucleotide.
  • differential expression refers to quantitative and/or qualitative differences in the expression of a gene or a protein in diseased tissue or cells versus normal tissue or cells.
  • a differentially expressed gene may have its expression activated or completely inactivated in normal versus disease conditions, or may be up-regulated (over-expressed) or down-regulated (under-expressed) in a disease condition versus a normal condition.
  • a gene or protein is differentially expressed when expression of the gene or protein occurs at a higher or lower level in the diseased tissues or cells of a patient relative to the level of its expression in the normal (disease-free) tissues or cells of the patient and/or control tissues or cells.
  • biological sample refers to a sample obtained from an organism (e.g., a human patient) or from components (e.g., cells) of an organism.
  • the sample may be of any relevant biological tissue or fluid.
  • the sample may be a “clinical sample” which is a sample derived from a patient.
  • Such samples include, but are not limited to, sputum, blood, blood cells (e.g., white cells), amniotic fluid, plasma, semen, bone marrow, and tissue or fine needle biopsy samples, urine, peritoneal fluid, and pleural fluid, or cells therefrom.
  • Biological samples may also include sections of tissues such as frozen sections taken for histological purposes.
  • a biological sample may also be referred to as a “patient sample.”
  • compositions, use or method denotes that additional elements and/or method steps may be present, but that these additions do not materially affect the manner in which the recited composition, method or use functions.
  • Consisting of when used herein in connection with a composition, use or method, excludes the presence of additional elements and/or method steps.
  • a composition, use or method described herein as comprising certain elements and/or steps may also, in certain embodiments consist essentially of those elements and/or steps, and in other embodiments consist of those elements and/or steps, whether or not these embodiments are specifically referred to.
  • Sepsis generally refers to a clinical response to a suspected or proven infection. Sepsis may be defined, for example, as including two or more of the following symptoms: tachypnea or tachycardia; leukocytosis or leukopenia; and hyperthermia or hypothermia, and may manifest as a complex infectious and immunological disorder. Many other symptoms may or may not occur and have been defined by consensus meetings of physicians (see Bone R C, Balk R A, Cerra F B, et al. Chest 2009; 136(5 Suppl):e28), however none of these symptoms are specific for sepsis.
  • Sepsis may be complicated by organ failure and may require admission to an intensive care ward in which case it is termed “severe sepsis.”
  • severe sepsis When a patient, often in the emergency ward, acquires some of the early symptoms associated with sepsis, they are frequently considered to be suspected sepsis patients, which triggers a special hospital protocol for treatment.
  • 24-48 hours when infection is confirmed by microbiological tests or the patient acquires more severe symptoms including failure of one of more organs are they confirmed to have been “early stage sepsis” patients (see review in Lyle N H, et al., Annals of the New York Academy of Sciences 2014, 1323:101-14).
  • the invention relates to a plurality of genes regulated during sepsis, the expression profile of which serves to define endotoxin tolerance in a subject. Differences in expression of these genes, either up- or down-regulation depending on the gene in question, when compared to a control defines a gene signature that is indicative of endotoxin tolerance (an “Endotoxin Tolerance Signature”).
  • Endotoxin Tolerance Signature Non-limiting examples of endotoxin tolerance signature genes (ETSGs) that may be comprised by an Endotoxin Tolerance Signature in accordance with certain embodiments of the invention are provided in Table 1.
  • sequences of these genes can readily be obtained by one of skill in the art from publicly available databases, such as the GenBank database maintained by the National Center for Biotechnology (NCBI), for example, by searching using the provided gene symbols. These gene symbols are universally recognized by all databases including HGNC, Entrez Gene, UniProtKB/Swiss-Prot, OMIM, GeneLoc, and Ensembl; all aliases are defined by the Gene Cards database.
  • GenBank maintained by the National Center for Biotechnology
  • An Endotoxin Tolerance Signature may comprise all endotoxin tolerance signature genes (ETSGs) shown in Table 1, or it may comprise a subset of these genes.
  • the Endotoxin Tolerance Signature may comprise as few as two ETSGs and up to 99 of the ETSGs shown in Table 1.
  • the Endotoxin Tolerance Signature comprises at least three, at least four, at least five, at least six, at least seven, at least eight, or least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, or at least fifteen of the ETSGs of Table 1.
  • the Endotoxin Tolerance Signature comprises 15 or more ETSGs, for example, 20 or more, 25 or more or 30 or more ETSGs. In some embodiments, the Endotoxin Tolerance Signature comprises about 31 ETSGs of Table 1. In some embodiments, the Endotoxin Tolerance Signature comprises about 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 99 ETSGs.
  • the Endotoxin Tolerance Signature comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 of the ETSGs in Table 1.
  • the Endotoxin Tolerance Signature comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 ETSGs selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the Endotoxin Tolerance Signature comprises at least 15, at least 20, at least 25 or at least 30 ETSGs selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the Endotoxin Tolerance Signature comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or 31 ETSGs selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR, and may optionally comprise one or more other ETSGs from Table 1.
  • the Endotoxin Tolerance Signature comprises the ETSGs: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR, and may optionally comprise one or more other ETSGs from Table 1.
  • the change in expression of an ETSG may be defined by an expression change direction, which indicates whether the gene is up- or down-regulated in a subject with endotoxin tolerance when compared to expression of the ETSG in a control (or reference) sample.
  • a subject with endotoxin tolerance would show an upregulation of one or more of ADAMDEC1, ANKRD1, C19orf59, CA12, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CYP1B1, CYP27B1, DDIT4, DPYSL3, EGR2, EMR1, EMR3, FBP1, FCER1G, FCER2, FPR1, FPR2, GK, GPR137B, HBEGF, HIST1H1C, HIST2H2AA3, HIST2H2AC, HK2, HK3, HPSE, HSD11B1, IL3RA, ITGB8, KIAA1199, L
  • the change in expression of an ETSG may be optionally further defined by a minimum fold change in expression level over control.
  • up- or down-regulation of a given ETSG may be defined as an at least 1.5-fold change in the level of expression of the gene when compared to a control.
  • up- or down-regulation of a given ETSG may be defined as a 2-fold or greater change in the level of expression of the gene when compared to a control.
  • a control (or standard or reference) level of expression may be, for example, the level of expression of the ETSG in a sample from a healthy subject, or the level of expression of the ETSG in a non-endotoxin tolerant cell.
  • Certain embodiments of the invention relate to diagnostic methods that use the Endotoxin Tolerance Signature to determine whether a subject having or suspected of having sepsis has endotoxin tolerance and is, therefore, at risk of developing one or more of sepsis, severe sepsis and/or organ failure.
  • the subject is suspected of having sepsis and the method identifies the patient as having sepsis. In some embodiments, the subject is suspected of having sepsis and the method identifies the subject as being at risk of developing severe sepsis and/or organ failure. In certain embodiments, the subject is suspected of having sepsis and the method identifies the patient as having severe sepsis.
  • the diagnostic methods comprise detecting the expression of the genes comprised by the Endotoxin Tolerance Signature in a biological sample obtained from a test subject. Differences in expression of these genes when compared to a control are determined. A difference in expression of at least two of these genes in the defined expression change direction is indicative that the subject has, or is at risk of developing, one or more of sepsis, severe sepsis and/or organ failure.
  • a difference in expression of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, eleven or more, twelve or more, thirteen or more, fourteen or more, or fifteen or more of the ETSGs in the Endotoxin Tolerance Signature when compared to a control sample is indicative that the subject has, or is at risk of developing, one or more of sepsis, severe sepsis and/or organ failure.
  • a difference in expression of at least 15, at least 20, at least 25 or at least 30 of the ETSGs in the Endotoxin Tolerance Signature when compared to a control sample is indicative that the subject has, or is at risk of developing, one or more of sepsis, severe sepsis and/or organ failure.
  • a difference in expression of about 31 of the ETSGs in the Endotoxin Tolerance Signature when compared to a control sample is indicative that the subject has, or is at risk of developing, one or more of sepsis, severe sepsis and/or organ failure.
  • a difference in expression of at least 20% of the ETSGs in the Endotoxin Tolerance Signature when compared to a control sample is indicative that the subject has, or is at risk of developing, one or more of sepsis, severe sepsis and/or organ failure.
  • a difference in expression of 20% or more, 30% or more, 40% or more, 50% or more, 60% or more, 70% or more, 80% or more, or 90% or more of the ETSGs in the Endotoxin Tolerance Signature when compared to a control sample is indicative that the subject has, or is at risk of developing, one or more of sepsis, severe sepsis and/or organ failure.
  • a difference in expression of at least 35% of the ETSGs in the Endotoxin Tolerance Signature when compared to a control sample is indicative that the subject has, or is at risk of developing, one or more of sepsis, severe sepsis and/or organ failure.
  • a difference in expression of each of the ETSGs in an Endotoxin Tolerance Signature when compared to a control sample is indicative that the subject has, or is at risk of developing, one or more of sepsis, severe sepsis and/or organ failure, wherein the Endotoxin Tolerance Signature may comprise between two and about 99 ETSGs, for example, between about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25 or 30 and about 99 ETSGs.
  • a difference in expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 of the following ETSGs when compared to a control sample is indicative that the subject has, or is at risk of developing, one or more of sepsis, severe sepsis and/or organ failure: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the biological sample may comprise, for example, blood, plasma, serum, tissue, amniotic fluid, saliva, urine, stool, bronchoalveolar lavage fluid, cerebrospinal fluid, or cells (such as skin cells) or cellular extracts.
  • the expression of the ETSGs comprised by the Endotoxin Tolerance Signature may be determined by detection of an expression product of each gene.
  • the expression product may be, for example, RNA, cDNA prepared from RNA, or protein.
  • the expression product is RNA or cDNA, the entire sequence of the gene may be detected, or any definitive portion of the gene, for example, a sequence of 10 nucleotides or more, may be detected.
  • PCR polymerase chain reaction
  • RT reverse transcriptase-(RT) PCR
  • Q-beta replicase amplification Q-beta replicase amplification
  • ligase chain reaction nucleic acid sequence amplification
  • signal amplification Ampliprobe
  • light cycling differential display, Northern analysis, hybridization, microarrays, RNA-Seq, nucleic acid sequencing, MassArray analysis, and MALDI-TOF mass spectrometry
  • the diagnostic methods employ detectably labelled polynucleotides for detecting expression of the ETSGs.
  • the methods may further comprise one or more of isolation of nucleic acids from the sample, purification of the nucleic acids, reverse transcription of RNA, and/or nucleic acid amplification.
  • the polynucleotide probes used to determine expression of the ETSGs may be immobilized on a solid support, for example, as an array or microarray allowing for more rapid processing of the sample. Methods of preparing arrays and microarrays are well known in the art.
  • Affymetrix U133 GeneChipTM arrays (Affymetrix, Inc., Santa Clara, Calif.), Agilent Technologies genomic cDNA microarrays (Santa Clara, Calif.), and arrays available from Illumina, Inc. (San Diego, Calif.). These arrays have probe sets for the whole human genome immobilized on a chip, and can be used to determine up- and down-regulation of genes in test samples.
  • Custom-made arrays and microarrays for detecting pre-selected genes are also available commercially from a number of companies. Instruments and reagents for performing gene expression analysis are commercially available (for example, the Affymetrix GeneChipTM System). The expression data obtained from the analysis may then be input into an appropriate database for further analysis if necessary or desired.
  • the differentially expressed genes can be detected, after conversion to cDNAs by the use of Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry using, for example the Sequenom MassARRAY® system (see, for example, Kricka L J. Clin Chem 1999; 45:453-458).
  • MALDI-TOF Matrix-assisted laser desorption/ionization-time of flight
  • reference genes are genes that are consistently expressed in many tissue types, including cancerous and normal tissues, and thus are useful to normalize gene expression profiles. Determining the expression of reference genes in parallel with the genes in the Endotoxin Tolerance Signature provides further assurance that the techniques used for determination of the gene expression profile are working properly. Appropriate reference genes (also referred to herein as control genes and housekeeping genes) can be readily selected by the skilled person.
  • the expression levels determined for the ETSGs of the Endotoxin Tolerance Signature are compared to a suitable reference or control, which may be for example expression levels of the ETSGs in a biological sample from a healthy individual or expression levels of the ETSGs in a non-endotoxin tolerant cell.
  • the comparison may include, for example, a visual inspection and/or an arithmetic or statistical comparison of measurements and may take into account expression of any reference genes. Suitable methods of comparison to determine differences in expression levels of genes are well known in the art.
  • the diagnostic methods may be used as confirmatory diagnostics to standard sepsis diagnostic procedures. In some embodiments, the diagnostic methods may be used as a stand-alone diagnostic.
  • the diagnostic methods may be used to confirm sepsis in a subject suspected of having sepsis.
  • the subject may have already undergone one or more assessments to determine whether they meet the standard diagnostic criteria for sepsis, for example, microbial culture analysis, measurement of blood pressure, white blood cell count, measurement of temperature, measurement of respiratory rate, and/or measurement of heart rate.
  • the diagnostic method may be used to confirm sepsis in a patient having been diagnosed as having sepsis by standard diagnostic criteria.
  • the diagnostic method may be used to diagnose a patient with sepsis as having severe sepsis and/or being at risk of organ failure.
  • determining the level of expression of ETSGs in a biological sample comprises detecting the presence in the biological sample of a plurality of mRNAs encoded by a plurality of ETSGs.
  • detecting the presence in the sample of mRNAs encoded by the ETSGs comprises performing a reverse transcription reaction using mRNAs obtained from the biological sample to generate cDNA products, and contacting the cDNA products with nucleic acid probes that are capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by the ETSGs.
  • the methods comprise contacting cDNA products generated by a reverse transcription reaction using mRNAs obtained from a biological sample with a microarray comprising nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs.
  • the invention relates to methods of treating patients identified as having endotoxin tolerance, for example by using the diagnostic methods described herein, in order to reduce the risk that they will develop sepsis, severe sepsis and/or organ failure.
  • early identification of the immunological state of sepsis patients by the methods described herein helps to guide selection of an appropriate therapy.
  • the method of treatment comprises administering a therapeutically effective dose of at least one antibiotic that is indicated for the treatment of severe sepsis to the patient.
  • antibiotics for treating severe sepsis include, but are not limited to, glycopeptides (such as vancomycin, oritvancin or televancin) ceflasporins (such as ceftriaxone, cefotaxime, or cefepime), beta-lactams/beta-lactamase inhibitors (such as piperacillin-tazobactam, ticarcillin-clavulanate), carbapenems (such as imipenem or meropenem), quinolones and fluoroquinolones (such as ciprofloxacin, moxifloxacin or levofloxacin), aminoglycosides (such as gentamicin, tobramycin or amikacin), macrolides (such as azithromycin, clarithromycin or erythromycin) and monobactams (such as aztreonam), and various combinations thereof. Typically combinations comprise antibiotics from different classes.
  • glycopeptides such as vancomycin,
  • sepsis may be defined as a disease characterized by endotoxin tolerance-mediated immune dysfunction.
  • counteracting endotoxin tolerance in sepsis patients is a potential therapeutic approach to prevent or decrease the likelihood of the patient developing severe sepsis and/or organ failure.
  • the invention relates to methods of treating a patient with sepsis that comprise administering to the patient an agent that counteracts endotoxin tolerance.
  • the invention relates to a method of preventing or decreasing the risk of a patient developing severe sepsis and/or organ failure comprising administering to the patient an agent that counteracts endotoxin tolerance.
  • patients are identified as being at risk of developing sepsis, severe sepsis and/or organ failure by the diagnostic methods described herein.
  • the agent that counteracts endotoxin tolerance may be, for example, an immunotherapy.
  • the agent that counteracts endotoxin tolerance comprises immune cells.
  • agents that counteract endotoxin tolerance include, but are not limited to, interferon-gamma, CpG oligonucleotides alone or in combination with IL-10, anti-CD40 antibodies, inhibitors of STAT3, inhibitors of STATE, inhibitors of p50, inhibitors of NF ⁇ B, inhibitors of IKK ⁇ , imidazoquinolines and zoledronic acid.
  • Endotoxin tolerance may result in macrophages being “locked” into an M2 state.
  • the agent that counteracts endotoxin tolerance is capable of altering macrophage phenotype from M2 to M1, or M2 to M0 (which represents uncommitted macrophages).
  • the invention relates to methods of treating a patient with sepsis that comprise administering to the patient an agent that alters macrophage phenotype from M2 to M1. In some embodiments, the invention relates to a method of preventing or decreasing the risk of a patient developing severe sepsis and/or organ failure comprising administering to the patient an agent that alters macrophage phenotype from M2 to M1. In certain embodiments, patients are identified as being at risk of developing sepsis, severe sepsis and/or organ failure by the diagnostic methods described herein.
  • the agent capable of altering macrophage phenotype from M2 to M1 is selected from an immunotherapy, immune cells, interferon-gamma, CpG oligonucleotides alone or in combination with IL-10, anti-CD40 antibodies, inhibitors of STAT3, inhibitors of STATE, inhibitors of p50, inhibitors of NF ⁇ B, inhibitors of IKK ⁇ , imidazoquinolines and zoledronic acid.
  • Certain embodiments of the invention relate to a method for decreasing the risk of a subject developing severe sepsis comprising administering an effective amount of an agent that counteracts endotoxin tolerance to a subject in need thereof.
  • the subject has been diagnosed as being at risk for developing severe sepsis by a method disclosed herein.
  • Certain embodiments of the invention relate to a method for decreasing the risk of organ failure in a subject comprising administering an effective amount of an agent that counteracts endotoxin tolerance to a subject in need thereof.
  • the subject has been diagnosed as being at risk of organ failure by a method disclosed herein.
  • Certain embodiments of the invention relate to a method for treating sepsis, comprising administering an effective amount of an agent that counteracts endotoxin tolerance to a subject in need thereof.
  • the subject has been diagnosed as having sepsis by a method disclosed herein.
  • the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein may be an immunotherapy.
  • the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein comprises immune cells.
  • the immune cell is a syngeneic immune cell, for example, the cell may be from the subject to whom the immune cell is being administered.
  • the immune cell is an allogeneic immune cell, that is, from an individual other than the subject to whom the immune cell is being administered.
  • the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is interferon gamma.
  • the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is a CpG-oligonucleotide (ODN).
  • ODN CpG-oligonucleotide
  • the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is a combination of a CpG ODN and interleukin-10 (IL-10).
  • the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is an anti-CD40 antibody.
  • the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is an inhibitor of STAT3.
  • the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is an inhibitor of STAT-6. In one embodiment, the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is an inhibitor of p50. In one embodiment, the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is an inhibitor of NF ⁇ B. In one embodiment, the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is an inhibitor of I ⁇ . In one embodiment, the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is an immidazoqinolone. In one embodiment, the agent that counteracts endotoxin tolerance and finds use in methods disclosed herein is zoledonic acid.
  • Certain embodiments of the invention relate to methods for identifying a candidate agent for the treatment of sepsis by evaluating the effect of a test agent on the expression of the ETSGs comprised by an Endotoxin Tolerance Signature.
  • the ability of the test compound to affect expression of the ETSGs may be assessed for example by contacting a cell in vitro with the test compound, determining the expression of the ETSGs in the cell and comparing the expression of the ETSGs in the cell with the level of expression of the same ETSGs in a control cell.
  • ETSGs may be assessed by various methods known in the art as described herein and elsewhere.
  • the test cell may be an endotoxin tolerant cell and the control cell may be a non-endotoxin tolerant (normal) cell.
  • the pattern of expression (or gene signature) of the cell treated with the test agent substantially corresponds to the pattern of expression (or gene signature) of the control cell, this indicates that the test agent is a candidate agent for the treatment of sepsis.
  • substantially corresponds in this context, it is meant that expression of those ETSG that are upregulated in exotoxin tolerant cells is decreased and expression of those ETSGs that are downregulated in exotoxin tolerant cells is increased.
  • the level of expression of at least one of the ETSGs in the treated cell is within a predetermined margin of the level of expression of the same ETSG in the control cell. For example, within about ⁇ 25%, within about ⁇ 20%, within about ⁇ 15%, or within about ⁇ 10% of the level of expression of the same ETSG in the control cell.
  • the method may further comprise contacting the cell with an endotoxin for a sufficient time to induce endotoxin tolerance in the cell prior to contacting the cell with the test agent.
  • the endotoxin may be, for example, a bacterial lipopolysaccharide (LPS) or lipoteichoic acid or a combination thereof.
  • LPS bacterial lipopolysaccharide
  • the LPS or lipoteichoic acid may be in an isolated form, or may be provided by contacting the cell with a bacterium that naturally contains the LPS and/or lipoteichoic acid.
  • the amount of time required to induce endotoxin tolerance can be readily determined by the skilled person. More than one treatment with endotoxin may be required to induce endotoxin tolerance.
  • a time between about 12 and about 24 hours may be used, for example, about 14, about 16, about 18 or about 20 hours, and between one and three treatments with endotoxin.
  • the endotoxin used in each treatment may be the same or different.
  • the method of screening may include assessing the endotoxin tolerant cell for restoration of the ability to react to endotoxin, thus indicating that the test agent is capable of breaking tolerance in the cell.
  • the method of screening further comprises contacting a second cell with an agent known to counteract endotoxin tolerance, such as interferon-gamma, a CpG-oligonucleotide (with or without IL-10), an anti-CD40 antibody, an inhibitor of STAT3, an inhibitor of STAT6, an inhibitor of p50, an inhibitor of NF ⁇ B, an inhibitor of IKK ⁇ , an imidazoquinolone or zoledronic acid, and determining the expression of the same ETSGs in the second cell.
  • an agent known to counteract endotoxin tolerance such as interferon-gamma, a CpG-oligonucleotide (with or without IL-10), an anti-CD40 antibody, an inhibitor of STAT3, an inhibitor of STAT6, an inhibitor of p50, an inhibitor of NF
  • the method may further comprise assaying the test agent for the ability to alter macrophage phenotype from M2 to M1.
  • kits useful for detecting ETSGs as identified herein will comprise one or more reagents for determining expression of a plurality, for example two or more, ETSGs.
  • the kit will comprise a collection of reagents, for example, two or more, that are used together to perform a diagnostic method, or one or more steps of a diagnostic method, as described herein, and which are provided together, usually within a common packaging.
  • the one or more reagents for determining expression of an ETSG may comprise a gene specific probe that is capable of detecting an expression product of the ETSG (nucleic acid or protein) or the complement of a nucleic acid expression product.
  • Polynucleotide primers for reverse transcription of mRNA encoded by the ETSG, and/or for amplification of a nucleic acid sequence from the ETSG or from cDNA prepared from the ETSG encoded mRNA may also be provided in the kit.
  • the kit comprises gene specific probes for a plurality of ETSGs are selected from the ETSGs listed in Table 1.
  • the plurality of ETSGs comprise C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • a kit comprises gene specific probes for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 of the ETSGs in Table 1.
  • the gene specific probes of a kit that are specific for ETSGs comprise probes for ETSGs selected from Table 1.
  • the gene specific probes of a kit that are specific for ETSGs consist of probes for ETSGs selected from Table 1.
  • the gene specific probes of a kit that are specific for ETSGs consists of probes for all the ETSGs in Table 1.
  • the gene specific probes of a kit that are specific for ETSGs comprise probes for ETSGs selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the gene specific probes of a kit that are specific for ETSGs consist of probes for ETSGs selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the gene specific probes of a kit that are specific for ETSGs consist of probes for each of the following: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • a kit comprises gene specific probes for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 of the following ETSGs: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • ETSGs C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PS
  • the kit may comprise or consist of a microarray that comprises a plurality of ETSG specific polynucleotide probes immobilized onto a solid support.
  • the microarray may further comprise control polynucleotide probes specific for control sequences, such as housekeeping genes.
  • the kit may optionally include one or more other reagents required to conduct a biological procedure, such as buffers, salts, enzymes, enzyme co-factors, substrates, detection reagents, washing reagents, and the like. Additional components, such as buffers and solutions for the isolation and/or treatment of a test sample, may also be included in the kit.
  • the kit may additionally include one or more control sequences or samples.
  • kits may optionally be lyophilised and the kit may further comprise reagents suitable for the reconstitution of the lyophilised component(s).
  • the container may itself be a suitable vessel for carrying out the biological procedure, for example, a microtitre plate.
  • the kit may also optionally contain reaction vessels, mixing vessels and other components that facilitate the preparation of reagents or a test sample, or the carrying out of the biological procedure.
  • the kit may also include one or more instruments for assisting with obtaining a test sample, such as a syringe, pipette, forceps, or the like.
  • reagents comprised by the kit or their containers may be colour-coded to facilitate their use.
  • reagents are colour-coded, addition of one reagent to another in a particular step may for example result in a change in the colour of the mixture, thus providing an indication that the step was carried out.
  • the kit can optionally include instructions for use, which may be provided in paper form, in computer-readable form, such as a CD, DVD, USB stick or the like, or in the form of directions or instructions for accessing a website.
  • the kit may also comprise computer readable media comprising software, or directions or instructions for accessing a website that provides software, to assist in the interpretation of results obtained from using the kit.
  • the microarrays comprise a plurality of polynucleotide probes attached to a solid support, each of the polynucleotide probes capable of specifically hybridizing to an expression product (or complement thereof) of a respective one of the plurality of ETSGs.
  • the microarray may optionally include one or more control probes, for example, probes capable of detecting the expression of housekeeping genes.
  • the microarray may further comprise probes for a plurality of Inflammatory Signature genes, for example, selected from those identified in Table 4.
  • probe sequences are typically between about 15 and about 100 nucleotides in length, for example, between about 15 and about 90 nucleotides in length, between about 15 and about 80 nucleotides in length, between about 15 and about 70 nucleotides in length, between about 15 and about 60 nucleotides in length, or between about 20 and about 60 nucleotides in length.
  • probe sequences comprise about 25 nt in Affymetrix arrays, and about 60 nt in Agilent arrays.
  • the microarray comprises a plurality of nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs.
  • the microarray consists essentially of nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs. In some embodiments, the microarray consists essentially of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, and (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a partial set of non-ETSGs.
  • the microarray consists essentially of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, and (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a partial set of housekeeping genes.
  • the microarray consists essentially of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, and (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of Inflammatory Signature genes.
  • the microarray consists essentially of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of Inflammatory Signature genes, and (iii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a partial set of housekeeping genes.
  • the microarray consists essentially of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of Inflammatory Signature genes, and (iii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a partial set of non-ETSGs.
  • the microarray consists of nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs. In some embodiments, the microarray consists of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, and (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a partial set of non-ETSGs.
  • the microarray consists of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, and (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a partial set of housekeeping genes.
  • the microarray consists of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, and (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of Inflammatory Signature genes.
  • the microarray consists of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of Inflammatory Signature genes, and (iii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a partial set of housekeeping genes.
  • the microarray consists of (i) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs, (ii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of Inflammatory Signature genes, and (iii) nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a partial set of non-ETSGs.
  • the number of nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by a plurality of ETSGs is greater than the number of other nucleic acid probes of the microarray. In some embodiments, the number of nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by ETSGs plus the number of nucleic acid probes capable of hybridizing to cDNAs that comprise nucleotide sequences complementary to mRNAs encoded by Inflammatory Signature genes is greater than the number of other nucleic acid probes of the microarray.
  • the plurality of ETSGs are selected from the ETSGs listed in Table 1.
  • the plurality of ETSGs comprise C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of Inflammatory Signature genes are selected from the genes listed in Table 4.
  • a microarray includes probes for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 of the ETSGs in Table 1.
  • the plurality of probes of a microarray that are specific for ETSGs comprise probes for ETSGs selected from Table 1.
  • the plurality of probes of a microarray that are specific for ETSGs consists of probes for ETSGs selected from Table 1.
  • the plurality of probes of a microarray that are specific for ETSGs consists of probes for all the ETSGs in Table 1.
  • the plurality of probes of a microarray that are specific for ETSGs comprises probes for ETSGs selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • probes for ETSGs selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2,
  • the plurality of probes of a microarray that are specific for ETSGs consists of probes for ETSGs selected from C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the plurality of probes of a microarray that are specific for ETSGs consists of probes for each of the following: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • a microarray includes probes for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 of the following ETSGs: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • ETSGs C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PS
  • a method of identifying a patient who has severe sepsis or is at high risk of developing severe sepsis comprising obtaining a biological sample from the individual and determining the level of expression of at least two or more genes from the endotoxin tolerance signature whereby the risk of sepsis, severe sepsis or organ failure is indicated by the altered expression of endotoxin tolerance signature genes relative to the expression of the same genes in non-sepsis individuals.
  • the invention provides a method of identifying a patient who has severe sepsis or is at high risk of developing severe sepsis, comprising obtaining a biological sample from the patient and determining the level of expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen different Endotoxin Tolerance Signature Genes (ETSGs) in the biological sample, whereby the presence or high risk of severe sepsis is indicated by the level of expression of the ETSGs. In one embodiment the level of expression of more than 15 different ETGSs is determined.
  • ETSGs Endotoxin Tolerance Signature Genes
  • the level of expression of more than 20 different ETGSs is determined. In one embodiment the level of expression of more than 25 different ETGSs is determined. In one embodiment the level of expression of more than 30 different ETGSs is determined. In one embodiment the level of expression of about 31 different ETGSs is determined.
  • the level of expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 of the ETSGs in Table 1 is determined.
  • the level of expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 of the following ETSGs is determined: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, REIN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the method further comprises determining the level of expression of the same ETSGs in a control sample from an individual who does not have sepsis. Where the expression levels of the ETSGs from the patient sample and the control sample are different, the patient is identified as having severe sepsis or being at high risk for severe sepsis.
  • the patient has not yet been definitively diagnosed as having severe sepsis. In another embodiment, the patient has already been diagnosed with severe sepsis.
  • the biological sample is selected from a group consisting of blood, tissue, amniotic fluid, saliva, urine, amniotic fluid, bronchoalveolar lavage fluid, and skin cells.
  • the identification of a patient with severe sepsis is used to guide optimal therapy for the patient.
  • the level of ETSG expression is determined by assessing the RNA or cDNA level in the biological sample. In one embodiment, the level of ETSG expression is determined using one or more methods selected from the polymerase chain reaction (PCR), reverse transcriptase-(RT) PCR, Q-beta replicase amplification, ligase chain reaction, nucleic acid sequence amplification, signal amplification (Ampliprobe), light cycling and other variations of PCR or non-PCR based amplification methods, differential display, Northern analysis, hybridization, microarrays, DNA sequencing, RNA-Seq, nucleic acid sequencing, MassArray analysis, and MALDI-TOF mass spectrometry.
  • PCR polymerase chain reaction
  • ligase chain reaction ligase chain reaction
  • nucleic acid sequence amplification amplification
  • signal amplification Ampliprobe
  • the invention provides a method of identifying an individual who is at risk of organ failure, comprising obtaining a biological sample from the individual and determining the level of expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen different ETSGs in the biological sample whereby the risk of organ failure is indicated by the level of expression of the ETSGs.
  • the level of expression of more than 15 different ETGSs is determined.
  • the level of expression of more than 20 different ETGSs is determined.
  • the level of expression of more than 25 different ETGSs is determined.
  • the level of expression of more than 30 different ETGSs is determined.
  • the level of expression of about 31 different ETGSs is determined.
  • the method further comprises determining the level of expression of the same ETSGs in a control sample from an individual who does not have sepsis. Where the expression levels of the ETSGs from the patient sample and the control sample are different, the patient is identified as having a risk of organ failure.
  • the level of expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 of the ETSGs in Table 1 is determined.
  • the level of expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 of the following ETSGs is determined: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the invention provides a method for treating severe sepsis, comprising identifying a patient who has severe sepsis or is at high risk of developing severe sepsis and treating said patient with at least one potent antibiotic that is indicated for the treatment of severe sepsis.
  • patient identification comprises obtaining a biological sample from the patient and determining the level of expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen different ETSGs in the biological sample, whereby the presence or high risk of severe sepsis is indicated by the level of expression of said at least two ETSGs.
  • the level of expression of more than 15 different ETGSs is determined.
  • the level of expression of more than 20 different ETGSs is determined.
  • the level of expression of more than 25 different ETGSs is determined.
  • the level of expression of more than 30 different ETGSs is determined.
  • the level of expression of about 31 different ETGSs is determined.
  • the level of expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 of the ETSGs in Table 1 is determined.
  • the level of expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 of the following ETSGs is determined: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • the method further comprises determining the level of expression of the same ETSGs in a control sample from an individual who does not have sepsis. Where the expression levels of the ETSGs from the patient sample and the control sample are different, the patient is identified as having severe sepsis and a therapeutically effective dose of at least one potent antibiotic that is indicated for the treatment of severe sepsis is administered to the patient.
  • the invention provides a test kit for the identification of severe sepsis, comprising at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of a different ETSG.
  • the kit comprises more than 15 different nucleic acids.
  • the kit comprises more than 20 different nucleic acids.
  • the kit comprises more than 25 different nucleic acids.
  • the kit comprises more than 30 different nucleic acids.
  • the kit comprises about 31 different nucleic acids.
  • the kit comprises at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of a different ETSG, wherein the ETSGs are selected from the group consisting of RNASE1, ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2,
  • the kit comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of a different ETSG in Table 1.
  • the kit comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of one of the following ETSGs: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • ETSGs C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H
  • the invention provides a test kit for identifying an individual who is at high risk of developing severe sepsis, comprising at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of a different ETSG.
  • the kit comprises more than 15 different nucleic acids.
  • the kit comprises more than 20 different nucleic acids.
  • the kit comprises more than 25 different nucleic acids.
  • the kit comprises more than 30 different nucleic acids.
  • the kit comprises about 31 different nucleic acids.
  • the kit comprises at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of a different ETSG, wherein the ETSGs are selected from the group consisting of RNASE1, ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2,
  • the kit comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of a different ETSG in Table 1.
  • the kit comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of one of the following ETSGs: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • ETSGs C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H
  • the invention provides a test kit for identifying an individual who is at risk of organ failure, comprising at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of a different ETSG.
  • the kit comprises more than 15 different nucleic acids.
  • the kit comprises more than 20 different nucleic acids.
  • the kit comprises more than 25 different nucleic acids.
  • the kit comprises more than 30 different nucleic acids.
  • the kit comprises about 31 different nucleic acids.
  • the kit comprises at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of a different ETSG, wherein the ETSGs are selected from the group consisting of RNASE1, ADAM15, ADAMDEC1, ALCAM, ALDH1A1, ANKRD1, C19orf59, CA12, CAMP, CCL1, CCL19, CCL22, CCL24, CCL7, CD14, CD300LF, CD93, CDK5RAP2, CPVL, CST3, CST6, CTSK, CXCL10, CYP1B1, CYP27B1, DDIT4, DHRS9, DPYSL3, EGR2,
  • the kit comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of a different ETSG in Table 1.
  • the kit comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 different nucleic acids, each of which comprises a nucleotide sequence that corresponds to or is complementary to the nucleotide sequence of one of the following ETSGs: C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H2AA3, HK2, HK3, HPSE, LILRA5, MGST1, PDLIM7, PLAUR, PSTPIP2, RAB13, RETN, RHBDD2, S100A4, S100A9, S100A12, SERPINA1, UPP1, CPVL, CST3, LY86 and PROCR.
  • ETSGs C19orf59, CCL22, CD14, CD300LF, CYP1B1, DHRS9, FCER1G, FPR1, FPR2, GK, HISTH2H
  • test kits of the invention further comprise instructions for use, a sample collection device, one or more reagents for sample preparation, and a positive control sample.
  • test kits of the invention further comprise instructions for use, a sample collection device, one or more reagents for sample preparation, and a negative control sample.
  • test kits of the invention further comprise instructions for use, a sample collection device, one or more reagents for sample preparation, and a negative control sample and a positive control sample.
  • the invention provides a method of treating a patient with severe sepsis, comprising administering to the patient a therapeutically effective amount of an agent that counteracts endotoxin tolerance by changing the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in a cell from the individual.
  • the agent is selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STAT6, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • the agent is an immune cell.
  • the invention provides a method of preventing or delaying severe sepsis in a patient, comprising administering to the patient an effective amount of an agent that counteracts endotoxin tolerance by changing the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or up to 99 different ETSGs in a cell from the patient.
  • the agent is selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STAT6, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • the agent is an immune cell.
  • the invention provides a method of treating severe sepsis in a patient, comprising administering to the patient a therapeutically effective amount of an agent that counteracts endotoxin tolerance by changing the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in a cell from the patient, and further comprises monitoring the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in samples taken from the patient during therapy.
  • the agent is selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STAT6, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • the agent is an immune cell.
  • the invention provides a method of preventing or delaying severe sepsis in a patient, comprising administering to the patient an effective amount of an agent that counteracts endotoxin tolerance by changing the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in a cell from the patient, and further comprises monitoring the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in samples taken from the patient during preventative treatment.
  • the agent is selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STAT6, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • the agent is an immune cell.
  • the invention provides a method of preventing or delaying organ failure in a patient, comprising administering to the patient an effective amount of an agent that counteracts endotoxin tolerance by changing the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in a cell from the patient, and further comprises monitoring the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in samples taken from the patient during preventative treatment.
  • the agent is selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STAT6, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • the agent is an immune cell.
  • the invention provides a method of treating severe sepsis, comprising administering to a patient a therapeutically effective amount of an agent selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STAT6, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • an agent selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STAT6, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • the method further comprises monitoring the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in samples taken from the patient during therapy.
  • the invention provides a method of preventing or delaying severe sepsis, comprising administering to a patient an effective amount of an agent selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STAT6, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • an agent selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STAT6, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • the method further comprises monitoring the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in samples taken from the patient during preventative treatment.
  • the invention provides a method of preventing or delaying organ failure, comprising administering to a patient an effective amount of an agent selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STATE, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • an agent selected from the group consisting of Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; inhibitors of STAT3, STATE, p50 NF ⁇ B, and IKK ⁇ ; imidazoquinolones; and zoledronic acid.
  • the method further comprises monitoring the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in samples taken from the patient during preventative treatment.
  • the invention provides a method of identifying an agent that is capable of treating sepsis, comprising contacting a cell with the agent and determining the expression of at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen different ETSGs in the cell.
  • the cell is an endotoxin tolerant cell. In one embodiment, the method further comprises contacting the cell with an endotoxin following contact of the cell with agent. In one embodiment, the endotoxin is bacterial lipopolysaccharide or lipoteichoic acid. In one embodiment, the bacterial lipopolysaccharide or lipoteichoic acid is present in a bacterium.
  • agents of the invention are obtained by contacting a cell with a suitable dose of endotoxin, waiting 18 hours and then contacting the cell again with a similar dose of the same or another endotoxin to create an endotoxin tolerant cell, then incubating the endotoxin tolerant cell with an agent of the invention and examining the restoration of cellular ability to interact with a third dose of endotoxin (breaking tolerance).
  • the method further comprises contacting a second cell with Interferon gamma; CpG-ODN with or without IL-10; anti-CD40; an inhibitor of STAT3, STAT6, p50 NF ⁇ B, or IKK ⁇ ; an imidazoquinolone; or zoledronic acid, and determining the expression of the same ETSGs in the second cell.
  • the method further comprises assaying the agent for the ability to alter macrophage phenotype from M2 to M1.
  • Agents of the invention may be obtained by contacting a cell with a suitable dose of endotoxin, waiting 18 hours and then contacting the cell again with a similar dose of the same or another endotoxin to create an endotoxin tolerant cell, then incubating the endotoxin tolerant cell with an agent of the invention and examining the restoration of cellular ability to interact with a third dose of endotoxin (breaking tolerance).
  • the endotoxin is bacterial lipopolysaccharide or lipoteichoic acid.
  • the invention provides an agent capable of treating sepsis, which agent is identified by a method of the invention.
  • the agent is capable of altering macrophage phenotypes from M2 to M1.
  • the invention provides a method for treating sepsis by suppressing endotoxin tolerance.
  • an agent that is capable of changing the expression of at least one, or at least two, or at least three, or at least four, or at least five, or at least six, or at least seven, or at least eight, or at least nine, or at least ten, or at least eleven, or at least twelve, or at least thirteen, or at least fourteen, or at least fifteen, or at least 31 different ETSGs in a cell from a patient is used.
  • Endotoxin Tolerance and Inflammatory LPS gene signatures were derived from published [Pena O M, et al. Journal of Immunology 2011; 186:7243-54] microarray analyses of human PBMC identifying differentially expressed genes compared to control PBMCs. To enable more direct comparisons between signatures, differentially expressed inflammatory genes were further reduced from 178 to 93 genes by overlap with an experimental endotoxaemia microarray dataset (GSE3284) [Calvano et al., Nature, 2005, 437:1032-1037] from the PBMC of healthy individuals stimulated with low-dose LPS in vivo at 2 and 6 hours.
  • GSE3284 experimental endotoxaemia microarray dataset
  • RNA Seq study reported here, 73 patients (age 60 ⁇ 17; 46 males, 27 females) were recruited with deferred consent according to UBC human ethics approval at the time of first examination in an emergency ward based on the opinion of physicians that there was a potential for the patient's condition to develop into sepsis. After the first blood draw, total RNA was prepared from whole blood, converted to cDNA, sequenced on an Illumina Genome Analyzer IIx, mapped to the human genome and converted into expression Tables by standard methods. Normalization used the Limma package function voom. All other clinical parameters based on routine tests were obtained by examination of patient's charts.
  • GEO Gene Expression Omnibus
  • Array Platform was A. GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array; B. GPL6947 Illumina HumanHT-12 V3.0 expression beadchip. STUDY DESIGN by study in column 1 of Table 2: 1.
  • GSE 13015 Cross-sectional.
  • GSE 9692 Cross-sectional. Children ⁇ 10 yr of age admitted to the pediatric intensive care unit (PICU), with pediatric-specific criteria for septic shock. Normal control patients were recruited from the participating institutions using the following exclusion criteria: a recent febrile illness (within 2 wk), recent use of anti-inflammatory medications (within 2 wks), or any history of chronic or acute disease associated with inflammation. 4. GSE 26378. Cross-sectional. Expression data from children with septic shock was generated using whole blood-derived RNA samples representing the first 24 hours of admission to the PICU.
  • Healthy subjects (children) were used as normal controls in the study. 5.
  • GSE 26440. Cross-sectional. Expression data from children with septic shock were generated using whole blood-derived RNA samples representing the first 24 hours of admission to the PICU. Healthy subjects (children) were used as normal controls in the study. 6.
  • GSE 4607. Longitudinal. Children ⁇ 10 years of age admitted to the pediatric intensive care unit and meeting the criteria for either SIRS or septic shock were eligible for the study. Control patients were recruited from the outpatient or inpatient departments of the participating institutions using the following exclusion criteria: a recent febrile illness (within 2 weeks), recent use of anti-inflammatory medications (within 2 weeks), or any history of chronic or acute disease associated with inflammation. 7.
  • GSE 8121. Longitudinal.
  • SIRS system
  • Clinical data was stored in an ORACLE-based database on a firewalled, RSS encrypted server at St Paul's Hospital.
  • Clinical data was collected retrospectively by physician researchers blinded to the RNA-Seq data. New organ dysfunction was defined based on laboratory values collected in the electronic medical record system. Acute organ failures assessed were the presence of shock (treatment with a vasopressor), acute respiratory distress syndrome (need for mechanical ventilation), coagulopathy (platelet count ⁇ 80/ ⁇ L), hepatic failure (total bilirubin >34 ⁇ mol/L) and acute kidney injury (a serum creatinine rise ⁇ 26.5 ⁇ mol/L or ⁇ 1.5 fold from baseline. Initial vital signs were retrospectively extracted from the paper records.
  • RNA-Seq was performed on a GAIIx instrument (Illumina), using a single read run with 63 bp long sequence reads (+adapter/index sequences).
  • Raw basecall data was converted to FASTQ sequence files using Off-Line Basecaller 1.9.4 (Ilumina) and a custom Perl script.
  • Reads were aligned to the hg19 human genome with TopHat version 2.06 and Bowtie2 2.0.0-beta6. Reads were initially mapped to Ensembl transcripts with the search for novel junctions disabled. Genomic coordinates were then transformed into counts of protein-coding Ensembl genes. To do this, a chimeric gene-model was first defined by merging all protein-coding transcripts for a given gene. Transcripts that had reads in less than 50% of their exons in all samples were defined as not expressed and were excluded from the chimeric transcriptome. Reads that overlapped the chimeric genes were counted using the htseq-count script in the intersection-nonempty mode (see EMBL website). The script discards multi-mapped reads as well as reads that overlap multiple distinct genes, to generate a file of uniquely mapped gene counts.
  • Endotoxin Tolerance and Inflammatory gene signatures were derived from previously published [Pena et al 2011] microarray analyses of human PBMC identifying differentially expressed genes compared to control PBMCs. To enable more direct comparisons between signatures, differentially expressed inflammatory genes were further reduced from 178 to 93 genes using an experimental endotoxaemia microarray dataset (GSE3284) obtained from the PBMC of healthy individuals stimulated in vivo with low-dose LPS for 2 and 6 hours. Importantly the two primary gene expression datasets (GSE22248 & GSE3284) used to derive signatures were then excluded from subsequent gene-set validation tests.
  • ROAST Gene set tests essentially ask whether a given gene set/signature is signature enriched in a dataset.
  • the ROAST method additionally allows for the consideration of a gene's direction of expression when calculating the enrichment, which increases the accuracy of the test in cases where the direction of the gene's expression is known (Wu et al., Bioinformatics, 20101 26(17):2176-82).
  • ROAST was run with 99999 rotations and so the most significant p-value resulting from this test is 0.00001.
  • ICU admission may depend on the inherent subjectivity of hospital regulations, such as space or number of beds available in each department, patients that are moved to the ICU are generally in a deteriorating condition with an increased risk of mortality. Therefore, the requirement for ICU admission was also assessed as a second, less precise measure of disease severity and showed that the Endotoxin Tolerance Signature was again associated with increased disease severity ( FIG. 6B ). These results indicate that endotoxin tolerance is associated with sepsis severity and specifically the subsequent development of organ failure.
  • the classification algorithm randomForest was used to assess the ability of the genes in the identified 31-gene subset to classify sepsis patients from controls.
  • Each dataset (external and internal) was divided into training and test sets and randomForest classification was performed independently on each dataset.
  • the 31-gene subset showed excellent accuracy when separating sepsis patients from controls with an average accuracy of 95.7% across all datasets (Table 6).
  • the 31-gene subset also showed strong performance in predicting sepsis and individual/combined organ failure in a group of patients with a suspicion of sepsis, with accuracies ranging from 62.4-87.4% (Table 6).
  • both the full 99-gene Endotoxin Tolerance Signature and the 31-gene subset will have utility as a tool in sepsis diagnosis.
  • Accurate diagnostic tools for sepsis are of high clinical priority due to the importance of early intervention in sepsis and the lack of clinical features specific to sepsis [Hotchkiss R S, Monneret G, Payen D. Lancet Infectious Diseases 2013; 13: 260-8].
  • An additional benefit to using endotoxin tolerance-related biomarkers is that they would also provide information regarding the patients' immune functional status.
  • the model was defined on the training set and then assessed on the test set using the randomForest package with ntree set to 1000. The procedure was repeated 1000 times, and the average prediction accuracies recorded for each data set. This analysis was repeated on the dataset to classify patients with an initial suspicion of sepsis who did or did not go on to develop sepsis or organ failure.
  • Sepsis is generally classified as an excessive inflammatory response (early stage), followed by a transition to an anti-inflammatory/immunosuppression dominated stage (Hotchkiss et al, 2013).
  • the nature and timing of this later stage had not been well characterized.
  • the results described herein revealed that all 10 sepsis patient cohorts showed an immunological expression profile strongly associated with the Endotoxin Tolerance Signature and subset and throughout all stages of early clinical disease ( FIGS. 2, 5 & 6 ). From a general clinical perspective, characterizing the nature and timing of the excessive inflammatory and anti-inflammatory/immunosuppression stages is essential when considering how to treat this disease.
  • the endotoxin tolerance-driven state is contributing to the overall immune dysfunction in sepsis and thus the severity of the disease.
  • the major cause of the immune dysfunction in sepsis is likely the rapid accumulation of tolerized monocytes/macrophages, locking the system into an M2-like state (Pena, O M, et al., J Immunol 2011, 186:7243-7254) in an attempt to reduce excessive neutrophilic inflammation and its consequences, such as vascular leakage, coagulation, lymphocyte death, etc.
  • weakening the patient's monocyte/macrophage responses can also lead to an inability to clear the primary infection and increased susceptibility to secondary infections, despite the continued activation of other immune cell populations, such as neutrophils.
  • neutrophils Due to their continuous replenishment from the bone marrow, neutrophils are probably the main drivers of pro-inflammatory cytokine responses, although they too are likely to eventually enter an endotoxin tolerant state (Parker L C, et al., J Leukocyte Biology 2005; 78:1301-1305).
  • a second therapeutic strategy would be to try to break tolerance, reversing the immunosuppressive state of macrophages.
  • virtually all therapies tried to treat sepsis have been in an attempt to do the opposite, i.e. suppress a hyperinflammatory state and this has the potential to worsen the patient's ability to defend against sepsis. Consistently, in more than 31 clinical trials to suppress the hyperinflammatory state, this approach has failed.
  • Examples of methods to break endotoxin tolerance include immune cells [Heusinkveld M, et al. Journal of Immunology 2011; 187:1157-1165], interferon gamma, CpG-ODN with or without IL-10, anti-CD40, inhibitors of STAT3, inhibitors of STATE, inhibitors of p50, inhibitors of NF ⁇ B, inhibitors of IKK ⁇ , imidazoquinolones and zoledronic acid [Sica A, A Mantovani. Journal of Clinical Investigation 2012; 122:787-795].
  • Other potential agents include those chemical agents, cells or natural products that suppress the expression of one or more genes from the Endotoxin Tolerance Signature in M2 polarized macrophages, or to revert the properties of M2 macrophages in vitro and in vivo to those of an M1 macrophage [Sica and Mantovani, 2012].

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