Diagnosis of sepsis or SIRS using biomarker profiles

• US 20040096917A1
• Filed: 11/12/2003
• Published: 05/20/2004
• Est. Priority Date: 11/12/2002
• Status: Abandoned Application

• Current Assignee: Becton, Dickinson & Co
• Original Assignee: Becton, Dickinson & Co
• Inventors: Garrett, James, Tice, Gregory, Shi, Song, Moore, Richard L., Bachur, Nicholas Jr., Nadeau, James G., Gentle, Thomas M. Jr., Rosenstein, Robert W., Goldenbaum, Paul E., Copertino, Donald, Ivey, Richard M., Towns, Michael L.
• Application Number:
  US10/704,899
• Publication Number:
  US 20040096917A1
• Time in Patent Office: Days
• US Class Current: 435/7.32
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G01N 2800/26 Infectious diseases, e.g. generalised sepsis
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins

Abstract

The early prediction or diagnosis of sepsis advantageously allows for clinical intervention before the disease rapidly progresses beyond initial stages to the more severe stages, such as severe sepsis or septic shock, which are associated with high mortality. Early prediction or diagnosis is accomplished by comparing an individual'"'"'s profile of biomarker expression to profiles obtained from one or more control, or reference, populations, which may include a population that develops sepsis. Recognition of features in the individual'"'"'s biomarker profile that are characteristic of the onset of sepsis allows a clinician to diagnose the onset of sepsis from a bodily fluid isolated from the individual at a single point in time. The necessity of monitoring the patient over a period of time is, therefore, avoided, advantageously allowing clinical intervention before the onset of serious symptoms of sepsis. Further, because the biomarker expression is assayed for its profile, identification of the particular biomarkers is unnecessary. The comparison of an individual'"'"'s biomarker profile to biomarker profiles of appropriate reference populations likewise can be used to diagnose SIRS in the individual.

Claims

1. A method of determining the status of sepsis in an individual, comprising:

(a) obtaining a first biomarker profile from a first biological sample taken from the individual; and

(b) comparing the individual'"'"'s first biomarker profile to a reference biomarker profile obtained from a reference population;

wherein a single such comparison is capable of classifying the individual as belonging to or not belonging to the reference population, and wherein the comparison determines the status of sepsis in the individual.

10. The method of claim 1, wherein the biological sample is selected from the group consisting of blood, saliva, serum, plasma, urine, stool, cerebral spinal fluid, cells, a cellular extract, a tissue sample, and a tissue biopsy.

11. The method of claim 1, further comprising:

(a) obtaining a second biomarker profile from a second biological sample taken from the individual; and

(b) comparing the individual'"'"'s second biomarker profile to the reference biomarker profile;

wherein the second comparison is capable of classifying the individual as belonging to or not belonging to the reference population, and wherein the second comparison determines the status of sepsis in the individual.

12. The method of claim 1, further comprising repeating the method at least once, wherein a separate biomarker profile is obtained from the individual from a separate biological sample taken each time the method is repeated.

13. The method of claim 12, wherein the biological samples from the individual are taken about 24 hours apart.

14. The method of claim 1, wherein the determining the status of sepsis in the individual comprises predicting the onset of sepsis in the individual.

15. The method of claim 14, wherein the onset of sepsis is predicted at least about 24 hours prior to the determination of sepsis in the individual using conventional techniques.

16. The method of claim 14, wherein the onset of sepsis is predicted at least about 48 hours prior to the determination of sepsis in the individual using conventional techniques.

17. The method of claim 14, wherein the onset of sepsis is predicted at least about 96 hours prior to the determination of sepsis in the individual using conventional techniques.

18. The method of claim 1, wherein the determining the status of sepsis in the individual comprises determining the progression of sepsis in the individual.

19. The method of claim 1, wherein the determining the status of sepsis in the individual comprises diagnosing sepsis in the individual.

20. The method of claim 1, wherein the comparison comprises applying a decision rule.

33. The method of claim 20, wherein the decision rule determines the status of sepsis in the individual with an accuracy of at least about 60%.

34. The method of claim 33, wherein the decision rule determines the status of sepsis in the individual with an accuracy of at least about 70%.

35. The method of claim 34, wherein the decision rule determines the status of sepsis in the individual with an accuracy of at least about 80%.

36. The method of claim 35, wherein the decision rule determines the status of sepsis in the individual with an accuracy of at least about 90%.

37. The method of claim 33, wherein the determination of the status of sepsis in the individual is made at least about 48 hours prior to clinical suspicion that the individual had sepsis, as determined using conventional techniques.

38. The method of claim 33, wherein the decision rule has been subjected to ten-fold cross-validation.

39. The method of claim 1, wherein the reference biomarker profile is obtained from a population comprising a single individual.

40. The method of claim 1, wherein the reference biomarker profile is obtained from a population comprising at least two individuals.

41. The method of claim 40, wherein the reference biomarker profile is obtained from a population comprising at least 20 individuals.

42. The method of claim 1, wherein the reference biomarker profile is obtained from a population selected from the group consisting of a normal reference population, a SIRS-positive reference population, an infected/SIRS-negative reference population, a sepsis-positive reference population, a reference population at a stage in the progression of sepsis, a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 0-36 hours, a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 36-60 hours, and a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 60-84 hours.

43. The method of claim 1, further comprising comparing a second biomarker profile from the individual with a reference biomarker profile, wherein the second biomarker profile is obtained from a second biological sample taken from the individual.

44. The method of claim 43, wherein the second biological sample from the individual is taken about 24 hours after the first biological sample is taken from the individual.

45. The method of claim 43, wherein the second biomarker profile is compared to a different reference biomarker profile than the first biomarker profile.

46. The method of claim 1, wherein the individual'"'"'s first biomarker profile and the reference biomarker profile comprise a measurable aspect of at least one nucleic acid.

47. The method of claim 46, wherein the nucleic acid is an mRNA.

48. The method of claim 1, wherein the individual'"'"'s first biomarker profile and the reference biomarker profile comprise a measurable aspect of at least one polypeptide.

49. The method of claim 48, wherein measurement of said measurable aspect comprises contacting the at least one polypeptide with an antibody or a functional fragment thereof that specifically binds the at least one polypeptide.

50. The method of claim 49, wherein said antibody or a functional fragment thereof is detectably labeled.

51. The method of claim 50, wherein the label is an amplifiable nucleic acid.

52. The method of claim 49, wherein the at least one polypeptide is present in blood.

53. The method of claim 49, wherein the at least one polypeptide is a cell surface protein.

54. The method of claim 49, wherein the at least one polypeptide is a component of a pathogen.

55. The method of claim 49, wherein the at least one polypeptide is an antibody that binds a component of a pathogen.

56. The method of claim 49, wherein the at least one polypeptide is an autoantibody.

57. The method of claim 1, comprising contacting proteins from the biological sample obtained from the individual with an array of antibodies, wherein the antibodies of the array are immobilized.

58. The method of claim 1, wherein said biological sample is fractionated prior to said obtaining of said individual'"'"'s first biomarker profile.

59. The method of claim 1, wherein at least one separation method is used to obtain said individual'"'"'s first biomarker profile.

60. The method of claim 59, wherein at least two separation methods are used to obtain said individual'"'"'s first biomarker profile.

61. The method of claim 59, wherein said at least one separation method comprises mass spectrometry.

62. The method of claim 61, wherein said mass spectrometry is selecting from the group consisting of electrospray ionization mass spectrometry (ESI-MS), ESI-MS/MS, ESI-MS/(MS)ⁿ, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS), desorption/ionization on silicon (DIOS), secondary ion mass spectrometry (SIMS), quadrupole time-of-flight (Q-TOF), atmospheric pressure chemical ionization mass spectrometry (APCI-MS), APCI-MS/MS, APCI-(MS)ⁿ, atmospheric pressure photoionization mass spectrometry (APPI-MS), APPI-MS/MS, and APPI-(MS)ⁿ, quadrupole mass spectrometry, fourier transform mass spectrometry (FTMS), and ion trap mass spectrometry, where n is an integer greater than zero.

63. The method of claim 62, wherein the at least one separation method comprises SELDI-TOF-MS.

64. The method of claim 59, wherein the at least one separation method is selected from the group consisting of chemical extraction partitioning, ion exchange chromatography, reverse phase liquid chromatography, isoelectric focusing, one-dimensional polyacrylamide gel electrophoresis (PAGE), two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), thin-layer chromatography, gas chromatography, liquid chromatography, and any combination thereof.

65. The method of claim 59, wherein at least two different separation methods are used to obtain said individual'"'"'s biomarker profile.

66. The method of claim 1, wherein said individual'"'"'s first biomarker profile and reference biomarker profile comprise a measurable aspect of an infectious agent or a component thereof.

67. The method of claim 66, wherein said component is selected from the group consisting of a viral coat protein, a lipopolysaccharide and lipoteichoic acid.

68. The method of claim 1, wherein said individual'"'"'s first biomarker profile and said reference biomarker profile comprise a measurable aspect of a biomarker that is informative of the state of the immune system in response to infection.

69. The method of claim 1, wherein said individual'"'"'s first biomarker profile and said reference biomarker profile comprise a measurable aspect of a biomarker selected from the group consisting of hormones, autoantibodies, growth factors, transcription factors, cell surface markers, and soluble proteins derived from cells.

70. The method of claim 1, wherein said individual'"'"'s first biomarker profile and said reference biomarker profile comprise a measurable aspect of a biomarker associated with bacteremia.

71. The method of claim 1, wherein said individual'"'"'s first biomarker profile and said reference biomarker profile comprise a measurable aspect of a biomarker associated with macrophage lysis.

72. The method of claim 1, wherein said individual'"'"'s first biomarker profile and said reference biomarker profile comprise a measurable aspect of a biomarker associated with a sepsis pathway.

73. The method of claim 1, wherein said individual'"'"'s first biomarker profile and said reference biomarker profile comprise a measurable aspect of an autoantibody.

74. The method of claim 1, wherein said individual'"'"'s first biomarker profile and said reference biomarker profile comprise a measurable aspect of a biomarker associated with a physiological condition selected from the group consisting of tissue hypoxia, multiple organ dysfunction, and metabolic acidosis.

91. The method of claim 20, wherein applying the decision rule comprises using a data analysis algorithm.

2. A method of determining the status of sepsis in an individual, comprising:

(a) obtaining a first biomarker profile at a single point in time from the individual; and

(b) comparing the individual'"'"'s first biomarker profile to a reference biomarker profile;

wherein the comparison of the biomarker profiles determines the status of sepsis in the individual with an accuracy of at least about 60%.

9. The method of claim 2, wherein the individual'"'"'s first biomarker profile is from a first biological sample from the individual, and the reference biomarker profile is from biological samples taken from the reference population.

3. A method of determining the status of sepsis in an individual, comprising comparing (i) a first biomarker profile generated from a first biological sample taken from the individual at a single point in time with (ii) a reference biomarker profile generated from a reference population, wherein the comparison comprises applying a decision rule that determines the status of sepsis in the individual.

21. The method of claim 3, wherein applying the decision rule comprises using a data analysis algorithm.

22. The method of claim 21, wherein the data analysis algorithm comprises the use of a classification tree.

23. The method of claim 21, wherein the data analysis algorithm is nonparametric.

24. The method of claim 23, wherein the data analysis algorithm detects differences in a distribution of feature values.

25. The method of claim 24, wherein the nonparametric algorithm comprises using a Wilcoxon Signed Rank Test.

26. The method of claim 21, wherein the data analysis algorithm comprises using a multiple additive regression tree.

27. The method of claim 21, wherein the data analysis algorithm is a logistic regression.

28. The method of claim 21, wherein the data analysis algorithm comprises at least two input parameters.

29. The method of claim 28, wherein the data analysis algorithm comprises at least five input parameters.

30. The method of claim 29, wherein the data analysis algorithm comprises at least ten input parameters.

31. The method of claim 30, wherein the data analysis algorithm comprises at least twenty input parameters.

32. The method of claim 21, wherein the data analysis algorithm uses at least two of the features set forth in any one of TABLES 15-23 and 26-50 as input parameters.

4. A method of determining the status of sepsis in an individual, comprising:

(a) obtaining a first biomarker profile from a first biological sample taken from the individual; and

(b) comparing the individual'"'"'s first biomarker profile to a reference biomarker profile obtained from biological samples from a reference population,

wherein the reference population is selected from the group consisting of a normal reference population, a SIRS-positive reference population, an infected/SIRS-negative reference population, a sepsis-positive reference population, a reference population at a stage in the progression of sepsis, a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 0-36 hours, a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 36-60 hours, and a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 60-84 hours, and wherein a single such comparison is capable of classifying the individual as belonging to or not belonging to the reference population, and wherein the comparison determines the status of sepsis in the individual.

5. A method of determining the status of sepsis in an individual, comprising comparing a measurable characteristic of at least one biomarker between (i) a first biomarker profile obtained from a first biological sample from the individual and (ii) a biomarker profile obtained from biological samples from a reference population, wherein the comparison classifies the individual as belonging or not belonging to the reference population, and wherein the comparison determines the status of sepsis in the individual.

6. A method of determining the status of sepsis in an individual, comprising:

(a) selecting at least two features from a set of biomarkers in a first biomarker profile generated from a first biological sample of an individual; and

(b) comparing the features to a set of the same biomarkers in a reference biomarker profile generated from biological samples from a reference population,

wherein a single such comparison is capable of classifying the individual as belonging to or not belonging to the reference population with an accuracy of at least about 60%, and wherein the comparison determines the status of sepsis in the individual.

7. A method of determining the status of sepsis in an individual, comprising:

(a) determining an abundance or changes in an abundance of at least two biomarkers in a first biomarker profile obtained from a first biological sample from the individual, and

(b) comparing the abundance or the changes in the abundance of the at least two biomarkers in the individual'"'"'s first biomarker profile to an abundance or changes in an abundance of these biomarkers in a reference biomarker profile obtained from biological samples from a reference population,

wherein the comparison is capable of classifying the individual as belonging to or not belonging to the reference population, and wherein the comparison determines the status of sepsis in the individual.

8. A method of determining the status of sepsis in an individual, comprising determining an abundance or a change in an abundance of at least one biomarker of a first biomarker profile obtained from a first biological sample from the individual as compared to an abundance or change in an abundance of the at least one biomarker of a reference biomarker profile obtained from biological samples from a (i) SIRS-positive reference population that contracted sepsis and (ii) a SIRS-positive reference population that did not, wherein the biomarkers are selected from the group consisting of the biomarkers listed in any one of TABLES 15-23 and 26-50.

75. A method of predicting the onset of sepsis in an individual, comprising:

(a) measuring an aspect of at least two features in a biomarker profile, wherein the biomarker profile comprises at least two biomarkers selected from the set of biomarkers set forth in any one of TABLES 15-23 and 26-50; and

(b) comparing the measured aspect of said at least two features with the value of a corresponding aspect of the same at least two features in a reference population,

wherein a single such comparison is capable of classifying the individual as belonging to or not belonging to the reference population, and wherein the comparison predicts the onset of sepsis in the individual.

76. The method of claim 75, wherein said prediction of the onset of sepsis is made about 12-36 hours prior to the onset of sepsis, where the onset of sepsis is determined by conventional techniques.

77. The method of claim 75, wherein said prediction of the onset of sepsis is made about 36-60 hours prior to the onset of sepsis, where the onset of sepsis is determined by conventional techniques.

78. The method of claim 75, wherein said prediction of the onset of sepsis is made about 60-84 hours prior to the onset of sepsis, where the onset of sepsis is determined by conventional techniques.

79. A method of diagnosing SIRS in an individual, comprising:

(a) obtaining a first biomarker profile from a first biological sample taken from the individual; and

(b) comparing the individual'"'"'s first biomarker profile to a reference biomarker profile obtained from a reference population,

wherein a single such comparison is capable of classifying the individual as belonging to or not belonging to the reference population, and wherein the comparison diagnoses SIRS in the individual.

80. A method of diagnosing SIRS in an individual, comprising:

(a) obtaining a biomarker profile at a single point in time from the individual; and

(b) comparing the individual'"'"'s biomarker profile to a reference biomarker profile,

wherein the comparison of the biomarker profiles can diagnose SIRS in the individual with an accuracy of at least about 60%.

81. A method of diagnosing SIRS in an individual, comprising comparing (i) a first biomarker profile generated from a first biological sample taken from the individual at a single point in time with (ii) a reference biomarker profile generated from a reference population, wherein the comparison comprises applying a decision rule that determines the status of SIRS in the individual.

82. A method of diagnosing SIRS in an individual, comprising:

(a) obtaining a first biomarker profile from a first biological sample taken from the individual; and

(b) comparing the individual'"'"'s first biomarker profile to a reference biomarker profile obtained from biological samples from a reference population,

wherein the reference population is selected from the group consisting of a normal reference population, a SIRS-positive reference population, and an infected/SIRS-negative reference population, a sepsis-positive reference population, a reference population at a stage in the progression of sepsis, a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 0-36 hours, a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 36-60 hours, and a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 60-84 hours, and wherein a single such comparison is capable of classifying the individual as belonging to or not belonging to the reference population, and wherein the comparison diagnoses SIRS in the individual.

83. A method of diagnosing SIRS in an individual, comprising comparing a measurable characteristic of at least one biomarker between (i) a first biomarker profile obtained from a first biological sample from the individual and (ii) a biomarker profile obtained from biological samples from a reference population, wherein the comparison classifies the individual as belonging or not belonging to the reference population, and wherein the comparison diagnoses SIRS in the individual.

84. A method of diagnosing SIRS in an individual, comprising:

(a) selecting at least two features from a set of biomarkers in a biomarker profile generated from a first biological sample of an individual; and

(b) comparing the features to a set of the same biomarkers in a biomarker profile generated from biological samples from a reference population,

wherein a single such comparison is capable of classifying the individual as belonging to or not belonging to the reference population with an accuracy of at least about 60%, and wherein the comparison diagnoses SIRS in the individual.

85. A method of diagnosing SIRS in an individual, comprising:

(a) determining an abundance or change in an abundance of at least two biomarkers contained in a first biological sample of an individual, and

(b) comparing the abundance or change in an abundance of the biomarkers in the individual'"'"'s sample to an abundance of these biomarkers in biological samples from a reference population,

wherein the comparison is capable of classifying the individual as belonging to or not belonging to the reference population, and wherein the comparison diagnoses SIRS in the individual.

86. A method of diagnosing SIRS in an individual, comprising determining the abundance or a change in abundance of at least one biomarker obtained from a biological sample from the individual as compared to an abundance or change in an abundance of the at least one biomarker obtained from biological samples from a normal reference population, wherein the biomarkers are selected from the group consisting of the biomarkers listed in any one of TABLES 15-23 and 26-50.

87. A method of isolating a biomarker, wherein said biomarker can be used to generate a biomarker profile to diagnose or predict sepsis, said method comprising:

(a) obtaining a reference biomarker profile, said reference biomarker profile obtained from a population of individuals;

(b) identifying a feature of said reference biomarker profile, wherein said feature is predictive or diagnostic of sepsis or one of the stages of sepsis;

(c) identifying a biomarker that corresponds with said feature; and

(d) isolating said biomarker.

88. A biomarker profile comprising at least two features that contribute to the classification of an individual as belonging to a reference population with an accuracy of at least about 60%, based on a comparison with the reference population, wherein the reference population is selected from the group consisting of a normal reference population, a SIRS-positive reference population, an infected/SIRS-negative reference population, a sepsis-positive reference population, a reference population at a stage in the progression of sepsis, a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 0-36 hours, a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 36-60 hours, and a SIRS-positive reference population confirmed as having sepsis by conventional techniques after about 60-84 hours.

89. A kit, comprising at least two biomarkers selected from the group consisting of the biomarkers listed in any one of TABLES 15-23 and 26-50.

90. A kit, comprising a set of antibodies or functional fragments thereof that specifically bind at least two biomarkers selected from the group consisting of the biomarkers listed in any one of TABLES 15-23 and 26-50.