U.S. patent application number 16/700098 was filed with the patent office on 2020-04-02 for biomarkers related to kidney function and methods using the same.
The applicant listed for this patent is Metabolon, Inc.. Invention is credited to Meredith V. Brown, Jeffery Edmond Cobb, Adam Kennedy, Regis Perichon.
Application Number | 20200103417 16/700098 |
Document ID | / |
Family ID | 51898805 |
Filed Date | 2020-04-02 |
![](/patent/app/20200103417/US20200103417A1-20200402-D00001.png)
![](/patent/app/20200103417/US20200103417A1-20200402-D00002.png)
![](/patent/app/20200103417/US20200103417A1-20200402-D00003.png)
![](/patent/app/20200103417/US20200103417A1-20200402-D00004.png)
![](/patent/app/20200103417/US20200103417A1-20200402-D00005.png)
![](/patent/app/20200103417/US20200103417A1-20200402-D00006.png)
United States Patent
Application |
20200103417 |
Kind Code |
A1 |
Perichon; Regis ; et
al. |
April 2, 2020 |
BIOMARKERS RELATED TO KIDNEY FUNCTION AND METHODS USING THE
SAME
Abstract
Biomarkers of kidney function and methods for using said
biomarkers for assessing kidney function, monitoring kidney
function, diagnosing acute kidney injury, and diagnosing chronic
kidney disease are provided. Also provided are suites of small
molecule entities as biomarkers for chronic kidney disease.
Inventors: |
Perichon; Regis; (Cary,
NC) ; Cobb; Jeffery Edmond; (Chapel Hill, NC)
; Brown; Meredith V.; (Durham, NC) ; Kennedy;
Adam; (Durham, NC) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Metabolon, Inc. |
Morrisville |
NC |
US |
|
|
Family ID: |
51898805 |
Appl. No.: |
16/700098 |
Filed: |
December 2, 2019 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
14889930 |
Nov 9, 2015 |
10539575 |
|
|
PCT/US2014/037762 |
May 13, 2014 |
|
|
|
16700098 |
|
|
|
|
61822965 |
May 14, 2013 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G01N 2800/347 20130101;
G01N 33/5308 20130101; G01N 2800/52 20130101; G01N 2800/56
20130101; G01N 33/70 20130101; G01N 2800/50 20130101; G01N 33/64
20130101; G01N 2570/00 20130101; G01N 33/6893 20130101; G01N
33/6848 20130101 |
International
Class: |
G01N 33/68 20060101
G01N033/68; G01N 33/53 20060101 G01N033/53; G01N 33/70 20060101
G01N033/70; G01N 33/64 20060101 G01N033/64 |
Claims
1. A method of assessing kidney function in a subject, the method
comprising: a) extracting small molecules from a biological sample
obtained from the subject to produce an analytical sample; b)
performing or having performed an assay on the analytical sample to
determine the level(s) of one or more biomarkers, wherein the one
or more biomarkers are selected from the group consisting of the
following biomarkers: N-acetylthreonine, N-acetylalanine, arabitol,
N-acetylserine, erythronate, 4-acetamidobutanoate,
N6-carbamoylthreonyladenosine, N-acetylcarnosine, arabonate,
xylonate, N-formylmethionine, O-methylcatechol sulfate,
N-acetylmethionine, N2,N5-diacetylornithine, ribose, pyroglutamine,
5-methylthioadenosine (MTA), 1-methylurate, pro-hydroxy-pro,
N-acetyl-3-methylhistidine, 2,3-dihydroxyisovalerate, trigonelline
(N'-methylnicotinate), X-11564, and X-17299; and c) assessing
kidney function in the subject by comparing the level(s) of the one
or more biomarkers to kidney function reference levels of the one
or more biomarkers in order to assess kidney function in the
subject.
2. The method of claim 1, further comprising performing or having
performed an assay on the analytical sample to determine the
level(s) of one or more additional biomarkers selected from the
group consisting of the following biomarkers:
trans-4-hydroxyproline, myo-inositol, kynurenine, tryptophan,
3-methylhistidine, erythritol, urea, 3-methylglutarylcarnitine
(C6), S-adenosylhomocysteine (SAH), N1-methyladenosine,
N2,N2-dimethylguanosine, p-cresol sulfate, succinylcarnitine,
2-methylbutyrylcarnitine (C5), N4-acetylcytidine,
N1-Methyl-2-pyridone-5-carboxamide, 1-methylhistidine, tiglyl
carnitine, isobutyrylcarnitine, indolelactate, glutarylcarnitine
(C5), choline, hydroxyisovaleroyl carnitine, scyllo-inositol,
quinate, salicyluric glucuronide, 2-mannopyranosyl tryptophan
(2-MPT), creatinine, phenylacetyl-L-glutamine, 3-indoxylsulfate,
pseudouridine, N6-acetyllysine, threitol and 2-hydroxyhippurate
(salicylurate).
3. The method of claim 1, further comprising using the determined
levels of the one or more biomarkers in a mathematical model to
calculate an estimated glomerular filtration rate (GFR) to
determine kidney function impairment.
4. The method of claim 3, wherein the sample is analyzed using one
or more techniques selected from the group consisting of mass
spectrometry, ELISA, and antibody linkage.
5. The method of claim 1, wherein the sample is obtained from a
subject that has no symptoms of impaired kidney function.
6. The method of claim 1, wherein the subject has been previously
diagnosed with hypertension and/or diabetes.
7. The method of claim 1, wherein the subject has symptoms of
impaired kidney function.
8. The method of claim 1, wherein the subject is one for whom
kidney function assessment using conventional methods is
difficult.
9. The method of claim 8, wherein the subject is selected from the
group consisting of the following: obese, very lean, vegetarian,
chronically ill, and elderly.
10. The method of claim 1, wherein the subject is a candidate to be
a kidney donor.
11. The method of claim 1, further comprising performing additional
analysis comprising BUN, serum creatinine (SCr), urine albumin
measurements, family history of chronic kidney disease (CKD),
.beta.-2 microglobulin, or .beta.-TRACE, and combining results of
the additional analysis with the assessment results from the
initial assessment steps.
12. A method of preventing impaired kidney function in a subject
being treated or considered for treatment with a composition,
wherein the composition may have a toxic effect on the kidneys, the
method comprising: a) extracting small molecules from a biological
sample obtained from the subject to produce an analytical sample;
b) performing, or having performed, an assay on the analytical
sample to determine the level(s) of one or more biomarkers, wherein
the one or more biomarkers are selected from the group consisting
of the following biomarkers: N-acetylthreonine, N-acetylalanine,
arabitol, N-acetylserine, erythronate, 4-acetamidobutanoate,
N6-carbamoylthreonyladenosine, N-acetylcarnosine, arabonate,
xylonate, N-formylmethionine, O-methylcatechol sulfate,
N-acetylmethionine, N2,N5-diacetylornithine, ribose, pyroglutamine,
5-methylthioadenosine (MTA), 1-methylurate, pro-hydroxy-pro,
N-acetyl-3-methylhistidine, 2,3-dihydroxyisovalerate, trigonelline
(N'-methylnicotinate), X-11564, and X-17299; and c) performing or
having performed an assay on the analytical sample to determine the
level(s) of one or more additional biomarkers selected from the
group consisting of the following biomarkers:
trans-4-hydroxyproline, myo-inositol, kynurenine, tryptophan,
3-methylhistidine, erythritol, urea, 3-methylglutarylcarnitine
(C6), S-adenosylhomocysteine (SAH), N1-methyladenosine,
N2,N2-dimethylguanosine, p-cresol sulfate, succinylcarnitine,
2-methylbutyrylcarnitine (C5), N4-acetylcytidine,
N1-Methyl-2-pyridone-5-carboxamide, 1-methylhistidine, tiglyl
carnitine, isobutyrylcarnitine, indolelactate, glutarylcarnitine
(C5), choline, hydroxyisovaleroyl carnitine, scyllo-inositol,
quinate, salicyluric glucuronide, 2-mannopyranosyl tryptophan
(2-MPT), creatinine, phenylacetyl-L-glutamine, 3-indoxylsulfate,
pseudouridine, N6-acetyllysine, threitol and 2-hydroxyhippurate
(salicylurate); and d) using the determined levels of the one or
more biomarkers and, optionally, the one or more additional
biomarkers, in a mathematical model to calculate an estimated
glomerular filtration rate (GFR); and e) using the estimated GFR to
assess kidney function in the subject being treated or considered
for treatment with the composition.
13. The method of claim 12, wherein the composition is selected
from the group consisting of a contrast imaging agent, a
chemotherapeutic agent, and an antibiotic.
14. A method of monitoring kidney function to prevent impaired
kidney function in a subject, the method comprising: a) extracting
small molecules from a biological sample obtained from a subject;
b) performing or having performed an assay on a first biological
sample from the subject to determine the level(s) of one or more
biomarkers for kidney function, where the one or more biomarkers
are selected from the group consisting of the following biomarkers:
N-acetylthreonine, N-acetylalanine, arabitol, N-acetylserine,
erythronate, 4-acetamidobutanoate, N6-carbamoylthreonyladenosine,
N-acetylcarnosine, arabonate, xylonate, N-formylmethionine,
O-methylcatechol sulfate, N-acetylmethionine,
N2,N5-diacetylornithine, ribose, pyroglutamine,
5-methylthioadenosine (MTA), 1-methylurate, pro-hydroxy-pro,
N-acetyl-3-methylhistidine, 2,3-dihydroxyisovalerate, trigonelline
(N'-methylnicotinate), X-11564, and X-17299; c) performing or
having performed the assay on a second biological sample from the
subject to determine the level(s) of the one or more biomarkers for
kidney function, wherein the second sample is obtained from the
subject at a second time point; and d) monitoring kidney function
in the subject by comparing the level(s) of one or more biomarkers
in the second sample to the level(s) of the one or more biomarkers
in (a) the first sample and/or (b) kidney function reference levels
of the one or more biomarkers.
15. The method of claim 14, further comprising performing or having
performed an assay on the first biological sample and the second
biological sample from the subject to determine the level(s) of one
or more additional biomarkers selected from the group consisting of
the following biomarkers: trans-4-hydroxyproline, myo-inositol,
kynurenine, tryptophan, 3-methylhistidine, erythritol, urea,
3-methylglutarylcarnitine (C6), S-adenosylhomocysteine (SAH),
N1-methyladenosine, N2,N2-dimethylguanosine, p-cresol sulfate,
succinylcarnitine, 2-methylbutyrylcarnitine (C5),
N4-acetylcytidine, N1-Methyl-2-pyridone-5-carboxamide,
1-methylhistidine, tiglyl carnitine, isobutyrylcarnitine,
indolelactate, glutarylcarnitine (C5), choline, hydroxyisovaleroyl
carnitine, scyllo-inositol, quinate, salicyluric glucuronide,
2-mannopyranosyl tryptophan (2-MPT), creatinine,
phenylacetyl-L-glutamine, 3-indoxylsulfate, pseudouridine,
N6-acetyllysine, threitol and 2-hydroxyhippurate
(salicylurate).
16. The method of claim 14, further comprising using the determined
levels of the one or more biomarkers in a mathematical model to
calculate an estimated glomerular filtration rate (GFR); and using
the estimated GFR to monitor kidney function.
17. The method of claim 14, wherein the subject is being treated
with a composition that may have a toxic effect on the kidneys.
18. The method of claim 17, wherein the composition is selected
from the group consisting of a contrast imaging agent, a
chemotherapeutic agent, or an antibiotic.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. National Stage
patent application Ser. No. 14/889,930, filed on Nov. 9, 2015,
which claims priority to International Patent Application No.
PCT/US2014/037762, filed on May 13, 2014, which claims the benefit
of U.S. Provisional Patent Application No. 61/822,965, filed May
14, 2013, the entire contents of which are all hereby incorporated
herein by reference.
FIELD
[0002] The invention generally relates to biomarkers for kidney
function and methods based on the same biomarkers.
BACKGROUND
[0003] There is a significant unmet clinical need for a sensitive,
accurate and convenient test to assess the excretory function of
the kidneys (glomerular filtration rate, GFR). The most accurate
measurement of renal function is the measured glomerular filtration
rate (mGFR), which requires the use of ideal filtration markers
(e.g., inulin, iothalamate, iohexol). Due to its complexity, this
measurement is expensive, difficult to perform in routine clinical
practice, and is typically only used in research studies or for
potential kidney donors. Consequently, alternative measures of
kidney function based on markers such as serum creatinine are used
in complex equations to derive an estimated GFR (eGFR). The
advantage of this approach is its ease of use in routine clinical
practice for the assessment of kidney function. However, these
methods of determining the GFR have limitations in truly assessing
the kidney function; some equations under-estimate GFR and some
over-estimate GFR, especially when it is in the "normal" range.
Some of these limitations are likely due to the variability of
serum creatinine levels which can be affected by muscle mass, diet,
and some drugs, including antibiotics, which leads to variable
levels among individuals and over time. The clinical consequence of
this inaccuracy leads to the misdiagnosis of patients. In some
cases, individuals with chronic kidney disease (CKD) are not
diagnosed by current methods and thus they do not receive
appropriate treatment (false negative). In other cases, individuals
may be diagnosed as having CKD when in fact they do not have CKD
(false positive); these individuals are then treated for a disease
they do not have. More recently serum levels of cystatin C have
been used to assess kidney function, but the utility of this
measure of kidney function is limited by the variability of
cystatin C serum levels among individuals. Thus, there is a need
for a convenient and more accurate test than the currently
available kidney function assessment tests to reduce the number of
false negative and false positive diagnoses.
[0004] Furthermore, current assessments of kidney function (e.g.,
serum creatinine, cystatin C and eGFR measurements, BUN, urine
albumin) are not sufficiently sensitive and/or accurate to detect
early kidney disease or to monitor its progression, especially at
the earliest stages of CKD when individuals are asymptomatic. Early
detection of declining kidney function could prevent significant
deterioration of kidney function that may occur before the problem
is detected with currently available methods. A novel test with a
sensitive readout that assesses and monitors an individual's kidney
function would allow for earlier detection of CKD, before CKD can
be detected with current methods. As a result, the overall cost of
treating and managing CKD and associated complications would be
reduced. With early detection of CKD, complications, including
cardiovascular disease, anemia, malnutrition and bone disease, can
be more effectively treated or possibly even prevented. Early
detection of CKD would enable lifestyle modifications such as
healthy diet, smoking cessation, weight loss, and treatment of high
blood pressure, which could prevent or reduce further kidney
injury, thereby reducing the need for dialysis and kidney
transplant which are frequent outcomes associated with reduced
kidney function and CKD.
[0005] A blood- or urine-based test to assess and/or monitor a
patient's renal function by measuring the level of one or more
biomarker metabolites in patients with risk factors for CKD (e.g.,
age over 60, hypertension, diabetes, cardiovascular disease, family
history of CKD) would be clinically useful. For example, the
biomarkers could comprise a test that quantitatively measures the
level of a panel of biomarker metabolites whereby the increase or
decrease in the level of each biomarker in the panel relative to a
standard reference level are indicative of kidney function. Such
biomarker test panels could replace or supplement current kidney
function test results and enable physicians to better assess kidney
function initially and/or to monitor kidney function in patients
over time. Such a test could also be useful in assessing the effect
of therapeutic interventions to slow kidney function decline.
SUMMARY
[0006] In one aspect, the present invention provides a method of
assessing or aiding in the assessment of kidney function,
comprising analyzing a biological sample from a subject to
determine the level(s) of one or more biomarkers for kidney
function in the sample, where the one or more biomarkers are
selected from the listed biomarkers: pseudouridine,
N-acetylthreonine, C-glycosyltryptophan, N-acetylserine,
N-acetylalanine, N6-carbamoylthreonyladenosine,
4-acetamidobutanoate, Erythritol, myo-inositol, erythronate, urea,
arabitol, N2,N2-dimethylguanosine, N1-methyladenosine,
3-methylglutarylcarnitine (C6), S-adenosylhomocysteine (SAH),
N-acetylmethionine, N6-acetyllysine, Kynurenine, arabonate,
succinylcarnitine, ribose, xylonite, N-formylmethionine,
O-methylcatechol sulfate, 2-methylbutyrylcarnitine (C5),
Phenylacetylglutamine, N2,N5-diacetylornithine, creatinine, and
comparing the level(s) of the one or more biomarkers in the sample
to kidney function reference levels of the one or more biomarkers
in order to assess the kidney function of a subject.
[0007] In another embodiment, the present invention provides a
method of assessing kidney function in response to a composition,
comprising analyzing a biological sample from a subject treated
with a composition to determine the level(s) of one or more
biomarkers for kidney function in the sample, where the one or more
biomarkers are selected from the listed biomarkers: pseudouridine,
N-acetylthreonine, C-glycosyltryptophan, N-acetylserine,
N-acetylalanine, N6-carbamoylthreonyladenosine,
4-acetamidobutanoate, erythritol, myo-inositol, erythronate, urea,
arabitol, N2,N2-dimethylguanosine, N1-methyladenosine,
3-methylglutarylcarnitine (C6), S-adenosylhomocysteine (SAH),
N-acetylmethionine, N6-acetyllysine, Kynurenine, arabonate,
succinylcarnitine, ribose, xylonite, N-formylmethionine,
O-methylcatechol sulfate, 2-methylbutyrylcarnitine (C5),
phenylacetylglutamine, N2,N5-diacetylornithine, creatinine, and
comparing the level(s) of the one or more biomarkers in the sample
to kidney function reference levels of the one or more biomarkers
in order to assess kidney function.
[0008] In another aspect, the present invention provides a method
of classifying or aiding in the classification of a subject
according to level of kidney function (e.g., normal, mildly
reduced, moderately reduced, severely reduced, end-stage kidney
failure) comprising analyzing a biological sample from a subject to
determine the level(s) of one or more biomarkers for kidney
function in the sample, where the one or more biomarkers are
selected from the listed biomarkers: pseudouridine,
N-acetylthreonine, C-glycosyltryptophan, N-acetylserine,
N-acetylalanine, N6-carbamoylthreonyladenosine,
4-acetamidobutanoate, Erythritol, myo-inositol, erythronate, urea,
arabitol, N2,N2-dimethylguanosine, N1-methyladenosine,
3-methylglutarylcarnitine (C6), S-adenosylhomocysteine (SAH),
N-acetylmethionine, N6-acetyllysine, Kynurenine, arabonate,
succinylcarnitine, ribose, xylonite, N-formylmethionine,
O-methylcatechol sulfate, 2-methylbutyrylcarnitine (C5),
Phenylacetylglutamine, N2,N5-diacetylornithine, creatinine, and
comparing the level(s) of the one or more biomarkers in the sample
to kidney function reference levels of the one or more biomarkers
in order to determine the level of kidney function of a
subject.
[0009] In another embodiment, the invention provides a method of
monitoring kidney function in a subject, the method comprising:
analyzing a first biological sample from a subject to determine the
level(s) of one or more biomarkers for kidney function, where the
one or more biomarkers are selected from the listed biomarkers:
pseudouridine, N-acetylthreonine, C-glycosyltryptophan,
N-acetylserine, N-acetylalanine, N6-carbamoylthreonyladenosine,
4-acetamidobutanoate, Erythritol, myo-inositol, erythronate, urea,
arabitol, N2,N2-dimethylguanosine, N1-methyladenosine,
3-methylglutarylcarnitine (C6), S-adenosylhomocysteine (SAH),
N-acetylmethionine, N6-acetyllysine, Kynurenine, arabonate,
succinylcarnitine, ribose, xylonite, N-formylmethionine,
O-methylcatechol sulfate, 2-methylbutyrylcarnitine (C5),
Phenylacetylglutamine, N2,N5-diacetylornithine, creatinine, and the
first sample is obtained from the subject at a first time point;
analyzing a second biological sample from a subject to determine
the level(s) of the one or more biomarkers, where the second sample
is obtained from the subject at a second time point; and comparing
the level(s) of one or more biomarkers in the second sample to the
level(s) of the one or more biomarkers in (a) the first sample, (b)
kidney function reference levels of the one or more biomarkers, (c)
CKD-positive reference levels of the one or more biomarkers, and/or
(d) CKD-negative reference levels of the one or more biomarkers in
order to monitor kidney function in the subject.
[0010] In a further embodiment, the invention provides a Kidney
Function Score to assess kidney function and/or to monitor kidney
function.
[0011] In another aspect, the present invention provides a method
of diagnosing or aiding in the diagnosis of CKD, comprising
analyzing a biological sample from a subject to determine the
level(s) of one or more biomarkers for kidney function in the
sample, where the one or more biomarkers are selected from Tables
1, 2, 3, and/or 4 and comparing the level(s) of the one or more
biomarkers in the sample to CKD-positive and/or CKD-negative
reference levels of the one or more biomarkers in order to
determine whether the subject has CKD.
[0012] In another embodiment, the methods described herein may be
used in combination with other methods (or the results thereof)
useful in the assessment of kidney function in a subject. For
example, clinical parameters such as BUN, SCr, and/or urine albumin
measurements; markers of kidney function such as .beta.-2
microglobulin, .beta.-TRACE, 2-mannopyranosyl tryptophan (2-MPT);
as well as patient information such as, for example, family history
of CKD or other risk factors can be used with the biomarkers.
[0013] In another embodiment, the methods described herein may be
used to assess kidney function and/or diagnose CKD in patients with
GFR estimates of 40-80 ml/min/1.73 m.sup.2.
[0014] In one embodiment, a biomarker panel comprised of
pseudouridine, C-glycosyltryptophan, N-acetylthreonine, and
creatinine may be used to assess kidney function and/or diagnose
CKD in a subject.
BRIEF DESCRIPTION OF THE DRAWINGS
[0015] FIG. 1 is an example of an algorithm for patient management
illustrating where the metabolite biomarker test (Novel
biomarker(s) test) would be useful to integrate into clinical
practice. Patients with eGFR and/or urine albumin scores in the
range for an uncertain diagnosis (as indicated in the hashed box)
would receive the metabolite biomarker test. Novel Biomarker Test
refers to a Metabolite Biomarker Kidney Function Test. G1: Stage 1
CKD, GFR>90; G2: Stage 2 CKD, GFR 60-89; G3a: Stage 3 CKD, GFR
45-59; G3b: Stage 3 CKD, GFR 30-44; G4: Stage 4 CKD, GFR 15-29; G5:
Stage 5 CKD, GFR<15 or on dialysis. A1: albumin-to-creatinine
ratio <30 mg/g; A2: albumin-to-creatinine ratio 30-300 mg/g; A3:
albumin-to-creatinine ratio >300 mg/g. CKD, chronic kidney
disease; eGFR, estimated glomerular filtration rate; SCr, serum
creatinine.
[0016] FIG. 2 is an example of an algorithm for patient management
when undergoing drug therapy showing the use of the metabolite
biomarker test. The level of kidney function would be assessed
using the metabolite biomarker test, and recommendations for the
drug therapy regimen could be made based on the results. Biomarker
Test refers to Metabolite Biomarker Kidney Function Test.
[0017] FIG. 3A is a graphical illustration of the distribution of
patient serum samples based on the level of C-glycosyltryptophan
measured in the sample as described in Example 2.
[0018] FIG. 3B is a graphical illustration of a ROC curve generated
using the exemplary biomarker C-glycosyltryptophan to distinguish
CKD from Normal as described in Example 2.
[0019] FIG. 4A is a graphical illustration of the distribution of
patient serum samples based on the level of N-acetylthreonine
measured in the sample as described in Example 2.
[0020] FIG. 4B is a graphical illustration of a ROC curve generated
using the exemplary biomarker N-acetylthreonine to distinguish CKD
from Normal as described in Example 2.
[0021] FIG. 5A is a graphical illustration of the distribution of
patient serum samples based on the level of pseudouridine measured
in the sample as described in Example 2.
[0022] FIG. 5B is a graphical illustration of a ROC curve generated
using the exemplary biomarker pseudouridine to distinguish CKD from
Normal as described in Example 2.
[0023] FIG. 6A is a graphical illustration of the correlation
analysis of the estimated GFR calculated using Model 1 described in
Example 3 with the eGFR calculated using the CKD-EPI equation.
[0024] FIG. 6B is a graphical illustration of the correlation
analysis of the estimated GFR calculated using Model 2 described in
Example 3 with the eGFR calculated using the CKD-EPI equation.
[0025] FIG. 6C is a graphical illustration of the correlation
analysis of the estimated GFR calculated using Model 3 described in
Example 3 with the eGFR calculated using the CKD-EPI equation.
[0026] FIG. 6D is a graphical illustration of the correlation
analysis of the estimated GFR calculated using Model 4 described in
Example 3 with the eGFR calculated using the CKD-EPI equation.
[0027] FIG. 6E is a graphical illustration of the correlation
analysis of the estimated GFR calculated using Model 5 described in
Example 3 with the eGFR calculated using the CKD-EPI equation.
DETAILED DESCRIPTION
[0028] Biomarkers of kidney function, methods of assessing or
aiding in the assessment of kidney function, methods for diagnosing
or aiding in the diagnosis of chronic kidney disease (CKD); methods
for classifying subjects according to level of kidney function;
methods of monitoring kidney function; methods of determining
susceptibility to CKD; methods of assessing kidney function in
response to a composition; as well as other methods based on
biomarkers of kidney function are described herein.
[0029] In one embodiment, groups (also referred to as "panels") of
biomarker metabolites that can be used to assess or aid in the
assessment of kidney function are identified.
[0030] Prior to describing this invention in further detail,
however, the following terms will be defined.
Definitions
[0031] "Biomarker" means a compound, preferably a metabolite, that
is differentially present (i.e., increased or decreased) in a
biological sample from a subject or a group of subjects having a
first phenotype (e.g., having a disease) as compared to a
biological sample from a subject or group of subjects having a
second phenotype (e.g., not having the disease). A biomarker may be
differentially present at any level, but is generally present at a
level that is increased by at least 5%, by at least 10%, by at
least 15%, by at least 20%, by at least 25%, by at least 30%, by at
least 35%, by at least 40%, by at least 45%, by at least 50%, by at
least 55%, by at least 60%, by at least 65%, by at least 70%, by at
least 75%, by at least 80%, by at least 85%, by at least 90%, by at
least 95%, by at least 100%, by at least 110%, by at least 120%, by
at least 130%, by at least 140%, by at least 150%, or more; or is
generally present at a level that is decreased by at least 5%, by
at least 10%, by at least 15%, by at least 20%, by at least 25%, by
at least 30%, by at least 35%, by at least 40%, by at least 45%, by
at least 50%, by at least 55%, by at least 60%, by at least 65%, by
at least 70%, by at least 75%, by at least 80%, by at least 85%, by
at least 90%, by at least 95%, or by 100% (i.e., absent). A
biomarker is preferably differentially present at a level that is
statistically significant (i.e., a p-value less than 0.05 and/or a
q-value of less than 0.10 as determined using either Welch's T-test
or Wilcoxon's rank-sum Test).
[0032] The "level" of one or more biomarkers means the absolute or
relative amount or concentration of the biomarker measured in the
sample.
[0033] "Sample" or "biological sample" means biological material
isolated from a subject. The biological sample may contain any
biological material suitable for detecting the desired biomarkers,
and may comprise cellular and/or non-cellular material from the
subject. The sample can be isolated from any suitable biological
tissue or fluid such as, for example, kidney tissue, blood, blood
plasma (plasma), blood serum (serum), urine, or cerebral spinal
fluid (CSF).
[0034] "Subject" means any animal, but is preferably a mammal, such
as, for example, a human, monkey, mouse, rabbit or rat.
[0035] A "reference level" of a biomarker means a level of the
biomarker that is indicative of a particular disease state,
phenotype, or lack thereof, as well as combinations of disease
states, phenotypes, or lack thereof. A "reference level" of a
biomarker may be an absolute or relative amount or concentration of
the biomarker, a presence or absence of the biomarker, a range of
amount or concentration of the biomarker, a minimum and/or maximum
amount or concentration of the biomarker, a mean amount or
concentration of the biomarker, and/or a median amount or
concentration of the biomarker; and, in addition, "reference
levels" of combinations of biomarkers may also be ratios of
absolute or relative amounts or concentrations of two or more
biomarkers with respect to each other. Appropriate reference levels
of biomarkers for a particular disease state, phenotype, or lack
thereof may be determined by measuring levels of desired biomarkers
in one or more appropriate subjects, and such reference levels may
be tailored to specific populations of subjects (e.g., a reference
level may be age-matched so that comparisons may be made between
biomarker levels in samples from subjects of a certain age and
reference levels for a particular disease state, phenotype, or lack
thereof in a certain age group). A "positive" reference level of a
biomarker means a level that is indicative of a particular disease
state or phenotype. A "negative" reference level of a biomarker
means a level that is indicative of a lack of a particular disease
state or phenotype. For example, a "CKD-positive reference level"
of a biomarker means a level of a biomarker that is indicative of a
positive diagnosis of CKD in a subject, and a "CKD-negative
reference level" of a biomarker means a level of a biomarker that
is indicative of a negative diagnosis of CKD in a subject (i.e.,
normal kidney function, absence of CKD). Likewise, a "kidney
function reference level" may indicate the degree of kidney
function present in a subject. For example, a "normal kidney
function reference level" of a biomarker means a level of a
biomarker that is indicative of normal kidney function in a
subject, a "moderately reduced kidney function reference level" of
a biomarker means a level of a biomarker that is indicative of
moderately reduced kidney function, and a "severely reduced kidney
function reference level" of a biomarker means a level of a
biomarker that is indicative of severely reduced kidney function in
a subject.
[0036] "Non-biomarker compound" means a compound that is not
differentially present in a biological sample from a subject or a
group of subjects having a first phenotype (e.g., having a first
disease) as compared to a biological sample from a subject or group
of subjects having a second phenotype (e.g., not having the first
disease). Such non-biomarker compounds may, however, be biomarkers
in a biological sample from a subject or a group of subjects having
a third phenotype (e.g., having a second disease) as compared to
the first phenotype (e.g., having the first disease) or the second
phenotype (e.g., not having the first disease).
[0037] "Metabolite", or "small molecule", means organic and
inorganic molecules which are present in a cell. The term does not
include large macromolecules, such as large proteins (e.g.,
proteins with molecular weights over 2,000, 3,000, 4,000, 5,000,
6,000, 7,000, 8,000, 9,000, or 10,000), large nucleic acids (e.g.,
nucleic acids with molecular weights of over 2,000, 3,000, 4,000,
5,000, 6,000, 7,000, 8,000, 9,000, or 10,000), or large
polysaccharides (e.g., polysaccharides with a molecular weights of
over 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, or
10,000). The small molecules of the cell are generally found free
in solution in the cytoplasm or in other organelles, such as the
mitochondria, where they form a pool of intermediates which can be
metabolized further or used to generate large molecules, called
macromolecules. The term "small molecules" includes signaling
molecules and intermediates in the chemical reactions that
transform energy derived from food into usable forms. Examples of
small molecules include sugars, fatty acids, amino acids,
nucleotides, intermediates formed during cellular processes, and
other small molecules found within the cell.
[0038] "Glomerular filtration rate" or "GFR" is the volume of fluid
filtered from the renal glomerular capillaries into the Bowman's
capsule per unit time. The GFR is a metric of kidney function
whereby GFR at or above a certain threshold indicates normal kidney
function and GFR below the threshold value indicates kidney
function is compromised or impaired. Generally, a high GFR value
indicates better kidney function while a low GFR indicates kidney
function impairment (e.g., chronic kidney disease, acute kidney
injury).
[0039] "Estimated glomerular filtration rate" or "eGFR" means a
calculated estimate of the actual glomerular filtration rate based
on serum creatinine concentration. Generally, low eGFR values are
associated with decreased kidney function.
[0040] "CKD-EPI eGFR" or "Chronic Kidney Disease Epidemiology
Collaboration" is an equation for calculating the eGFR. The
equation is: GFR=141.times.min(SCr/.kappa.,1).sup..alpha.
.times.max(SCr/.kappa.,1).sup.-1.209.times.0.993.sup.Age.times.1.018
[if female].times.1.159 [if black], where SCr is serum creatinine
(mg/dL), .kappa. is 0.7 for females and 0.9 for males, .alpha. is
-0.329 for females and -0.411 for males, min indicates the minimum
of SCr/.kappa. or 1, and max indicates the maximum of SCr/.kappa.
or 1.
[0041] "MDRD or "Modification of Diet in Renal Disease eGFR" is
another equation for calculating the eGFR. The equation is:
eGFR=186.times.(S.sub.cr).sup.-1.154.times.(Age).sup.-0.203.times.(0.742
if female).times. (1.212 if Black), where Scr is serum creatinine
(mg/dL).
[0042] "Urine albumin" is a test measuring the amount of albumin in
the urine and is also used to detect kidney disease.
[0043] "Serum creatinine" or "SCr" refers to the measurement of
creatinine in serum and is commonly used to estimate GFR.
[0044] "Blood urea nitrogen" or "BUN" refers to the measurement of
the amount of nitrogen in the blood in the form of urea. BUN is a
test used to measure kidney function.
[0045] "Chronic Kidney Disease" or "CKD" includes conditions that
damage kidneys resulting in decreased ability of the kidney to
remove wastes from the body resulting in high levels of the wastes
in the body and leading to increased risk of illness and
development of complications such as high blood pressure, anemia,
poor nutritional health and nerve damage. Patients with
abnormalities in kidney function for at least three months may be
diagnosed with CKD. Kidney damage due to CKD is permanent.
[0046] "Acute kidney injury" or "AKI" refers to a condition in
which there is a rapid loss of kidney function. Kidney damage due
to AKI may be reversible.
[0047] "Chronic Kidney Disease Stages" or "CKD Stages" means the
degree of kidney damage as currently assessed using the measured or
estimated glomerular filtration rate (mGFR, eGFR). Clinically, 5
stages of CKD are generally recognized with kidney function
regarded as normal in Stage 1 (GFR>90), minimally reduced in
Stage 2 (GFR 60-89), moderately reduced in Stages 3A and 3B (GFR
30-59), severely reduced in Stage 4 (GFR 15-29) and very severe or
endstage kidney failure, also referred to as established renal
failure at Stage 5 (GFR<15, or on dialysis). Kidney function
stages may be used to refer to kidney damage present for any amount
of time (i.e., kidney damage due to AKI or CKD).
I. Biomarkers
[0048] Generally, metabolic profiles were generated from biological
samples collected from human subjects with a range of kidney
function as determined by eGFR, as calculated using the CKD-EPI
eGFR equation and/or the MDRD eGFR equation. Biomarkers of kidney
function were identified by analyzing the levels of metabolites
measured in serum and urine samples from the subjects and
correlating the levels with eGFR; those molecules that correlated
significantly with eGFR were selected as biomarkers of kidney
function. Biomarkers of CKD, were identified by generating the
metabolic profile for biological samples collected from a group of
subjects having CKD (i.e., individuals with eGFR<60) and
comparing said profile to the metabolic profile for biological
samples from subjects not having CKD (i.e., individuals with
eGFR> or =60). Those molecules differentially present, including
those molecules differentially present at a level that is
statistically significant (p<0.1), in the metabolic profile of
serum samples from subjects with CKD as compared to the control
group (e.g., subjects not diagnosed with CKD) were identified as
biomarkers to diagnose CKD.
[0049] The biomarkers are discussed in more detail herein. The
identified biomarkers may be used to assess kidney function in a
subject, to monitor a subject to detect changes in kidney function
(e.g., decreases in function which may indicate acute kidney injury
or incipient CKD), to classify subjects according to the degree of
kidney function (e.g., normal, mildly reduced, moderately reduced,
severely reduced, end-stage kidney failure) and to distinguish
subjects having CKD vs. control subjects not diagnosed with CKD
(see Tables 1, 2, 3, and/or 4). Further, the biomarkers may be used
to monitor changes in kidney function over time or in response to
drug treatment, disease (e.g., type II diabetes), or lifestyle
interventions (e.g., diet, exercise) and to identify or rule-out
subjects as suitable candidates for drug therapies and/or kidney
transplant.
II. Methods
A. Assessing Kidney Function Using the Biomarkers
[0050] The kidney function biomarkers can be used to assess (or aid
in the assessment of) kidney function in a subject. It will be
understood that the identified biomarkers can be used to assess
kidney function in any subject and includes the assessment of
kidney function in an asymptomatic subject, in a subject at risk of
CKD or AKI due to the presence of symptoms, or risk factors (e.g.,
hypertension, diabetes, family history of CKD, exposure to certain
chemical/environmental conditions, etc.), and in a subject in
response to a composition or to a therapeutic intervention (e.g.,
kidney transplant, lifestyle modification). It is further
understood that a subject may undergo one or more assessments of
kidney function.
[0051] In an exemplary method, assessing kidney function in a
subject comprises (1) analyzing a biological sample obtained from a
subject to determine the level(s) of one or more biomarkers for
kidney function in the sample and (2) comparing the level(s) of the
one or more biomarkers in the sample to reference level(s) of the
one or more biomarkers to assess kidney function in a subject and
determine if kidney function is normal or impaired as well as to
determine the level of kidney function impairment. The one or more
biomarkers may be selected from Tables 1, 2, 3, and/or 4 and/or
from the group consisting of the following biomarkers:
pseudouridine, N-acetylthreonine, C-glycosyltryptophan,
N-acetylserine, N-acetylalanine, N6-carbamoylthreonyladenosine,
4-acetamidobutanoate, Erythritol, myo-inositol, erythronate, urea,
arabitol, N2,N2-dimethylguanosine, N1-methyladenosine,
3-methylglutarylcarnitine (C6), S-adenosylhomocysteine (SAH),
N-acetylmethionine, N6-acetyllysine, Kynurenine, arabonate,
succinylcarnitine, ribose, xylonite, N-formylmethionine,
O-methylcatechol sulfate, 2-methylbutyrylcarnitine (C5),
Phenylacetylglutamine, N2,N5-diacetylornithine, creatinine and
combinations thereof. When such a method is used to aid in
assessing kidney function, the results of the method may be used
along with other methods (or the results thereof) and/or patient
metadata useful in the clinical determination of whether a subject
has normal kidney function or impaired kidney function (which can
result from an acute kidney injury (AKI) or CKD) as well as the
level of kidney function (e.g., normal, mildly impaired, moderately
impaired, severely impaired, end-stage kidney failure).
[0052] Any suitable method may be used to analyze the biological
sample in order to determine the level(s) of the one or more
biomarkers in the sample. Suitable methods include chromatography
(e.g., HPLC, gas chromatography, liquid chromatography), mass
spectrometry (e.g., MS, MS-MS), enzyme-linked immunosorbent assay
(ELISA), antibody linkage, other immunochemical techniques, and
combinations thereof. Further, the level(s) of the one or more
biomarkers may be measured indirectly, for example, by using an
assay that measures the level of a compound (or compounds) that
correlates with the level of the biomarker(s) that are desired to
be measured.
[0053] The level of one or more of the biomarkers selected from the
listed biomarkers: pseudouridine, N-acetylthreonine,
C-glycosyltryptophan, N-acetylserine, N-acetylalanine,
N6-carbamoylthreonyladenosine, 4-acetamidobutanoate, Erythritol,
myo-inositol, erythronate, urea, arabitol, N2,N2-dimethylguanosine,
N1-methyladenosine, 3-methylglutarylcarnitine (C6),
S-adenosylhomocysteine (SAH), N-acetylmethionine, N6-acetyllysine,
Kynurenine, arabonate, succinylcarnitine, ribose, xylonite,
N-formylmethionine, O-methylcatechol sulfate,
2-methylbutyrylcarnitine (C5), Phenylacetylglutamine,
N2,N5-diacetylornithine, creatinine, may be determined in the
described methods. For example, the level(s) of one biomarker, two
or more biomarkers, three or more biomarkers, four or more
biomarkers, five or more biomarkers, six or more biomarkers, seven
or more biomarkers, eight or more biomarkers, nine or more
biomarkers, ten or more biomarkers, etc., including a combination
of all of the listed biomarkers.
[0054] Determining levels of combinations of the biomarkers may
allow greater sensitivity and specificity in the described methods.
For example, pair-wise analysis of two biomarkers or ratios of the
levels of certain biomarkers (and non-biomarker compounds) in
biological samples may allow greater sensitivity and specificity in
assessing kidney function and aiding in the assessment of kidney
function. For example, the ratio of myo-inositol to
glycerophosphocholine (GPC), tryptophan to kynurenine, tryptophan
to 3-indoxyl sulfate, and/or tryptophan to indoleacetate may be
used to assess kidney function in a subject. In further examples,
determining levels of combinations of two or more, three or more,
four or more, and/or five or more biomarkers may allow greater
sensitivity and specificity in the methods described herein. In one
example, the levels of pseudouridine, C-glycosyltryptophan,
N-acetylthreonine, and creatinine may be used to assess kidney
function in a subject. In another example, the levels of
pseudouridine, N-acetylthreonine, myo-inositol, and creatinine may
be used to assess kidney function in a subject. In another example,
the levels of N-acetylthreonine, myo-inositol,
C-glycosyltryptophan, and creatinine may be used to assess kidney
function in a subject. In another example, the levels of
N-acetylthreonine, myo-inositol, kynurenine, and creatinine may be
used to assess kidney function in a subject. In another example,
the levels of pseudouridine, C-glycosyltryptophan,
N-acetylthreonine, and myo-inositol may be used to assess kidney
function in a subject.
[0055] The level(s) of the one or more biomarkers may be compared
to kidney function reference levels using various techniques,
including a simple comparison (e.g., a manual comparison). The
level(s) of the one or more biomarkers in the biological sample may
also be compared to reference levels using one or more statistical
analyses (e.g., t-test, Welch's T-test, Wilcoxon's rank sum test,
correlation analysis, Random Forest, T-score, Z-score) or using a
mathematical model (e.g., algorithm, statistical model). For
example, a mathematical model comprising a single algorithm or
multiple algorithms may be used to assess kidney function in a
subject.
[0056] The results of the method may be used along with other
methods and measurements (or the results thereof) useful in the
assessment of kidney function in a subject. For example, clinical
parameters such as BUN, SCr, and/or urine albumin measurements;
markers of kidney function such as .beta.-2 microglobulin,
.beta.-TRACE, 2-mannopyranosyl tryptophan (2-MPT); as well as
patient information such as, for example, family history of CKD or
other risk factors can be used with the biomarkers.
[0057] In one example, the identification of biomarkers for kidney
function allows for the assessment of (or for aiding in the
assessment of) kidney function in patients undergoing imaging tests
using contrast agents where the contrast imaging agents may be
toxic and, as a result, may cause kidney injury. For example in a
patient with reduced kidney function (e.g., Stage 2 CKD or Stage 3
or Stage 3A CKD), an accurate measure of kidney function will help
patients and clinicians assess the risk to benefit ratio of imaging
tests and will allow for more informed decisions.
[0058] In another example, the identification of biomarkers for
kidney function allows for the assessment of (or for aiding in the
assessment of) kidney function to detect incipient CKD before CKD
can be diagnosed using the current standards for determining kidney
function (e.g., SCr, eGFR, cystatin C urine albumin and/or BUN
measurements). Clinical measures may not be sufficiently sensitive
to detect early changes in kidney function or may be inaccurate in
certain subjects due to, for example, chronic illness, obesity,
advanced age, vegetarian diet and/or generally reduced muscle mass.
For example, in a subject with type 2 diabetes, the biomarkers
described herein may be used to diagnose or aid in the diagnosis of
CKD. Accurate and early diagnosis of CKD may allow earlier
therapeutic intervention which could delay or prevent the
development of further kidney damage and more severe CKD.
[0059] In another example, an accurate assessment of kidney
function in a subject who is a potential kidney donor will aid a
physician in determining whether the potential donor is suitable
for donating a kidney.
[0060] In another example, the biomarkers provided allow for a
method of assessing kidney function in a subject being treated with
a composition. The composition may be any composition, drug or
therapeutic agent given to a subject to treat any disease or
condition. The composition additionally may be any composition
given to a patient having a disease or condition, for example, a
contrast imaging agent. For example, the identification of
biomarkers for kidney function also allows for assessment of the
subject's response to a composition that alters kidney function as
well as the assessment of the relative patient response to two or
more compositions that alter kidney function. Such assessments may
be used, for example, to select compositions for treating cancer
for certain subjects, or to select subjects for a course of
treatment or inclusion in clinical trial. Such assessments may also
be used to monitor kidney function in response to a composition
prior to, throughout and/or following (i.e., post-launch) the drug
development process.
[0061] In another embodiment, the instant invention allows for a
metabolite biomarker test to provide an accurate determination of
kidney function in patients with eGFR values that are borderline
normal thus enabling a clinician to select a certain treatment or
modify treatment of the patients to reduce the risk of further
kidney damage. Such a biomarker test overcomes limitations of
current kidney function tests which do not accurately assess all
patient populations, (often leading to false positive or false
negative diagnoses), and do not detect early kidney function
impairment (which may be indicative of AKI or incipient CKD). For
example, illustrated in FIG. 1 is an example clinical practice
algorithm (flow chart) that depicts best practices for screening,
diagnostic evaluation, treatment, and management of clinical
symptoms to diagnose CKD. Integrated into this flow chart is a
kidney function biomarkers test based on analyzing the levels of a
panel of biomarkers for kidney function selected from the listed
biomarkers: pseudouridine, N-acetylthreonine, C-glycosyltryptophan,
N-acetylserine, N-acetylalanine, N6-carbamoylthreonyladenosine,
4-acetamidobutanoate, Erythritol, myo-inositol, erythronate, urea,
arabitol, N2,N2-dimethylguanosine, N1-methyladenosine,
3-methylglutarylcarnitine (C6), S-adenosylhomocysteine (SAH),
N-acetylmethionine, N6-acetyllysine, Kynurenine, arabonate,
succinylcarnitine, ribose, xylonite, N-formylmethionine,
O-methylcatechol sulfate, 2-methylbutyrylcarnitine (C5),
Phenylacetylglutamine, N2,N5-diacetylornithine, and creatinine. In
this example, a patient with no symptoms of CKD may initially have
kidney function assessed by measuring SCr, and eGFR and/or urine
albumin as recommended by current clinical practice guidelines. CKD
stages of G2-G3a as measured by eGFR and/or CKD stage A1 as
measured by urine albumin often result in false positive or false
negative diagnoses; confirmatory testing is recommended. Patients
with these scores would receive the novel metabolite biomarker test
to aid in diagnosing CKD (hashed box). Levels of kidney function
biomarkers that are normal are indicative that the patient has
normal kidney function. Patients diagnosed as Normal using the
metabolite biomarker test would be monitored periodically to assess
kidney function. A result for which the metabolite biomarkers
levels at baseline are significantly above or below normal range
indicate that a patient has CKD. Patients diagnosed as having CKD
by using the metabolite biomarker test would receive appropriate
treatment.
[0062] In one aspect, the biomarkers provided herein can be used in
a mathematical or statistical model or formula to provide a
physician with a numerical score ("Kidney Function Score")
indicating the level of kidney function and/or the probability that
a subject has compromised kidney function which may indicate AKI or
CKD. The score is based upon clinically significantly changed
reference level(s) for a biomarker and/or combination of
biomarkers. The reference level can be derived from an algorithm or
computed from indices for impaired GFR. Methods for determining a
subject's Kidney Function Score may comprise comparing the level(s)
of the one or more kidney function biomarkers in the sample to
kidney function reference levels of the one or more biomarkers in
order to determine the subject's Kidney Function Score. The method
may employ any number of markers selected from the following list:
pseudouridine, N-acetylthreonine, C-glycosyltryptophan,
N-acetylserine, N-acetylalanine, N6-carbamoylthreonyladenosine,
4-acetamidobutanoate, Erythritol, myo-inositol, erythronate, urea,
arabitol, N2,N2-dimethylguanosine, N1-methyladenosine,
3-methylglutarylcarnitine (C6), S-adenosylhomocysteine (SAH),
N-acetylmethionine, N6-acetyllysine, Kynurenine, arabonate,
succinylcarnitine, ribose, xylonite, N-formylmethionine,
O-methylcatechol sulfate, 2-methylbutyrylcarnitine (C5),
Phenylacetylglutamine, N2,N5-diacetylornithine, and creatinine.
Multiple biomarkers may be correlated with kidney function, by any
method, including statistical methods such as regression
analysis.
[0063] The Kidney Function Score can be used to place the subject
in the range of kidney function from normal (i.e. no kidney
function impairment) to mildly reduced, moderately reduced,
severely reduced, or end-stage kidney failure. Non-limiting example
uses of the Kidney Function Score include: assessment of kidney
function; classification of kidney function; susceptibility to
developing CKD; susceptibility to developing AKI; diagnosis and
stage of CKD; monitoring CKD progression by periodic determination
and monitoring of the Kidney Function Score; monitoring the kidney
function status of kidney transplant recipients; determining a
response to therapeutic intervention; evaluating drug efficacy; and
determining tolerance of therapeutic and/or contrast imaging
agents.
[0064] In some embodiments, the methods may be used assess kidney
function over time, thereby enabling kidney function to be
monitored. The change (if any) in the level(s) of the one or more
biomarkers over time (i.e., in a first sample from a subject at a
first time point compared to a second sample obtained from the
subject at a second time point) may be indicative of altered kidney
function in the patient over time. To characterize the kidney
function of a subject over time, the level(s) of the one or more
biomarkers in the first sample, the level(s) of the one or more
biomarkers in the second sample, and/or the results of the
comparison of the levels of the biomarkers in the first and second
samples may be compared to reference levels of the one or more
biomarkers. If the comparisons indicate that the level(s) of the
one or more biomarkers are increasing or decreasing over time
(e.g., in the second sample as compared to the first sample) to
become more similar to the low kidney function reference levels (or
less similar to the high kidney function reference levels), then
the results are indicative of declining kidney function. If the
comparisons indicate that the level(s) of the one or more
biomarkers are increasing or decreasing over time to become more
similar to the high kidney function reference levels (or less
similar to the low kidney function reference levels), then the
results are indicative of normal kidney function. For example, a
subject may have normal kidney function at a first time point
(e.g., biomarker(s) is similar to the high kidney function
reference level or dissimilar to the low kidney function reference
level) and remains in the normal range at a second time point
(e.g., remains similar to the high kidney function reference
level(s) or dissimilar to the low kidney function reference
level(s)), indicating no change in kidney function. In another
instance, the kidney function may be normal at a first time point
(e.g., biomarker(s) is similar to the high kidney function
reference level(s) or dissimilar to the low kidney function
reference level(s)) then decreases at a second time point yet
remains in the normal range of kidney function, indicating that
although still in the normal range, the kidney function decreased.
In another illustration, a subject with borderline normal kidney
function at a first time point may be diagnosed with CKD based on
the level(s) of the biomarker(s) at the second time point
indicating a worsening of kidney function in the subject.
[0065] The difference between the relative amount of the biomarker
and the reference level may also be used to assess kidney function
over time. For example, if the comparisons indicate that there is a
larger difference between the level(s) of the one or more
biomarkers and the high kidney function reference levels (or a
smaller difference between the level(s) of the one or more
biomarkers and the low kidney function reference levels) over time,
then the results are indicative of the patient developing declining
kidney function.
[0066] After the first sample is obtained one or more additional
samples may be obtained from the subject at a later point in time.
In one aspect, the one or more additional samples are obtained 1,
2, 3, 4, 5, 6, or more days after the first sample. In another
aspect, the one or more samples is obtained 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, or more weeks after the first sample or after the initiation
of treatment with the composition. In another aspect, the one or
more additional samples may be obtained 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, or more months after the first sample or after the
initiation of treatment with the composition.
[0067] In another embodiment, the methods could be used to monitor
kidney function in subjects having CKD or subjects suspected of
being predisposed to developing CKD (e.g., at risk subjects due to
family history of CKD, drug therapy, chronic illness, etc.). In one
example, the biomarkers disclosed herein may be used to monitor
kidney function in subjects not having CKD. For example, in a
subject suspected of being predisposed to developing CKD, the
biomarkers described herein may be used to monitor the development
of CKD.
[0068] In another example, the biomarkers disclosed herein may be
used to monitor kidney function in kidney transplant
recipients.
[0069] In another embodiment, a biomarker algorithm could be used
to monitor a patient's kidney function. Using the results of the
biomarker algorithm in combination with current kidney function
test results (e.g., SCr, eGFR, BUN, urine albumin, cystatin C) a
clinician could assess the risk-benefit ratio of the drug treatment
in the patient. Additionally, a biomarker algorithm could be used
by clinicians treating any patient at risk for developing loss of
kidney function (e.g., diabetics, hypertensive, elderly, family
history, smokers, chronically ill, kidney transplant recipient,
etc.). The drug therapy may be any agent used to treat any disease
or condition.
[0070] Illustrated in FIG. 2 is an example of a biomarker algorithm
(flow chart). Levels of kidney function biomarkers that are normal
at baseline and remain within normal range during therapy, are
indicative that the patient has normal kidney function.
[0071] A result for which the levels of metabolite biomarkers at
baseline or the changes in these levels during therapy are outside
the normal range but not excessively so would indicate that a
patient has mild to moderate loss of kidney function. These
patients represent those whose results would be borderline with
current kidney function tests. Based on the result of the
metabolite biomarker test, the treating clinician may elect to
re-assess the risk-benefit of the current treatment regimen (e.g.,
therapeutic agent, dose) in the patient and change the patient's
management.
[0072] A result for which the levels of metabolite biomarkers at
baseline or the changes in these levels during therapy are
significantly and excessively outside normal range would indicate
that a patient has severe loss of kidney function. Changes to the
patient's management would be strongly advised (e.g., discontinue
treatment with particular drug, switch to another agent).
B. Diagnosing Chronic Kidney Disease Using the Biomarkers
[0073] The identification of biomarkers for kidney function also
allows for the diagnosis of (or for aiding in the diagnosis of) CKD
in a subject. It will be understood that the identified biomarkers
can be used to diagnose or aid in diagnosing CKD in any subject,
including asymptomatic subjects, those subjects presenting with one
or more symptoms consistent with the presence of CKD and/or those
subjects where CKD is probable (e.g., chronic illness, drug
treatments, use of contrast imaging agents, etc.). In an exemplary
method, diagnosing (or aiding in diagnosing) whether a subject has
CKD comprises (1) analyzing a biological sample from a subject to
determine the level(s) of one or more biomarkers of kidney function
in the sample and (2) comparing the level(s) of the one or more
biomarkers in the sample to CKD-positive and/or CKD-negative
reference levels of the one or more biomarkers in order to diagnose
(or aid in the diagnosis of) whether the subject has CKD. The one
or more biomarkers may be selected from Table 1. When such a method
is used to aid in the diagnosis of CKD, the results of the method
may be used along with other methods and measurements (or the
results thereof) and/or patient metadata useful in the clinical
determination of whether a subject has CKD. Methods useful in the
clinical determination of whether a subject has CKD are known in
the art. For example, methods useful in the clinical determination
of whether a subject has CKD include, for example, SCr, BUN, eGFR,
mGFR, urine albumin, and cystatin C. Other measurements useful in
determining whether a subject has CKD include, for example,
.beta.-2 microglobulin, .beta.-TRACE, and/or 2-mannopyranosyl
tryptophan (2-MPT). Patient metadata useful in the clinical
determination of whether a subject has CKD include, for example,
age, weight, gender, and race.
[0074] Any suitable method may be used to analyze the biological
sample in order to determine the level(s) of the one or more
biomarkers in the sample. Suitable methods include chromatography
(e.g., HPLC, gas chromatography, liquid chromatography), mass
spectrometry (e.g., MS, MS-MS), enzyme-linked immunosorbent assay
(ELISA), antibody linkage, other immunochemical techniques, and
combinations thereof. Further, the level(s) of the one or more
biomarkers may be measured indirectly, for example, by using an
assay that measures the level of a compound (or compounds) that
correlates with the level of the biomarker(s) that are desired to
be measured.
[0075] The level of one or more of the biomarkers of Table 1 may be
determined in the methods of assessing and methods of aiding in the
assessment of kidney function in a subject. For example, the
level(s) of one biomarker, two or more biomarkers, three or more
biomarkers, four or more biomarkers, five or more biomarkers, six
or more biomarkers, seven or more biomarkers, eight or more
biomarkers, nine or more biomarkers, ten or more biomarkers, etc.,
including a combination of any or all of the biomarkers in Table 1
or any fraction thereof, may be determined and used in such
methods.
[0076] Determining levels of combinations of the biomarkers may
allow greater sensitivity and specificity in diagnosing CKD and
aiding in the diagnosis of CKD. For example, pair-wise analysis of
two biomarkers or ratios of the levels of certain biomarkers (and
non-biomarker compounds) in biological samples may allow greater
sensitivity and specificity in diagnosing CKD and aiding in the
diagnosis of CKD. For example, the ratio of myo-inositol to
glycerophosphocholine (GPC), tryptophan to kynurenine, tryptophan
to 3-indoxyl sulfate, and/or tryptophan to indoleacetate may be
used to diagnose or aid in the diagnosis of CKD in a subject. In
another example, determining levels of combinations of two or more,
three or more, four or more, and/or five or more biomarkers may
allow greater sensitivity and specificity in the methods described
herein. In one example, the levels of pseudouridine,
C-glycosyltryptophan, N-acetylthreonine, and creatinine may be used
to diagnose or aid in the diagnosis of CKD in a subject. In another
example, the levels of pseudouridine, N-acetylthreonine,
myo-inositol, and creatinine may be used to diagnose or aid in the
diagnosis of CKD in a subject. In another example, the levels of
N-acetylthreonine, myo-inositol, C-glycosyltryptophan, and
creatinine may be used to diagnose or aid in the diagnosis of CKD
in a subject. In another example, the levels of N-acetylthreonine,
myo-inositol, kynurenine, and creatinine may be used to diagnose or
aid in the diagnosis of CKD in a subject. In another example, the
levels of pseudouridine, C-glycosyltryptophan, N-acetylthreonine,
and myo-inositol may be used to diagnose or aid in the diagnosis of
CKD in a subject.
[0077] After the level(s) of the one or more biomarkers in the
sample are determined, the level(s) are compared to CKD-positive
and/or CKD-negative reference levels to diagnose or to aid in
diagnosing whether the subject has CKD. Levels of the one or more
biomarkers in a sample matching the CKD-positive reference levels
(e.g., levels that are the same as the reference levels,
substantially the same as the reference levels, slightly above
and/or below the minimum and/or maximum of the reference levels,
and/or within the range of the reference levels) are indicative of
a diagnosis of CKD in the subject. Levels of the one or more
biomarkers in a sample matching the CKD-negative reference levels
(e.g., levels that are the same as the reference levels,
substantially the same as the reference levels, slightly above
and/or below the minimum and/or maximum of the reference levels,
and/or within the range of the reference levels) are indicative of
a diagnosis of no CKD in the subject. In addition, levels of the
one or more biomarkers that are differentially present (especially
at a level that is statistically significant) in the sample as
compared to CKD-negative reference levels are indicative of a
diagnosis of CKD in the subject. Levels of the one or more
biomarkers that are differentially present (especially at a level
that is statistically significant) in the sample as compared to
CKD-positive reference levels are indicative of a diagnosis of no
CKD in the subject.
[0078] The level(s) of the one or more biomarkers may be compared
to CKD-positive and/or CKD-negative reference levels using various
techniques, including a simple comparison (e.g., a manual
comparison) of the level(s) of the one or more biomarkers in the
biological sample to CKD-positive and/or CKD-negative reference
levels. The level(s) of the one or more biomarkers in the
biological sample may also be compared to CKD-positive and/or
CKD-negative reference levels using one or more statistical
analyses (e.g., t-test, Welch's T-test, Wilcoxon's rank sum test,
correlation analysis, Random Forest, T-score, Z-score) or using a
mathematical model (e.g., algorithm, statistical model).
[0079] For example, a mathematical model comprising a single
algorithm or multiple algorithms may be used to assess kidney
function in a subject. A mathematical model may also be used to
determine whether a subject has CKD. A mathematical model may also
be used to distinguish between CKD stages. An exemplary
mathematical model may use the measured levels of any number of
biomarkers (for example, 2, 3, 5, 7, 9, etc.) from a subject to
determine, using an algorithm or a series of algorithms based on
mathematical relationships between the levels of the measured
biomarkers, whether a subject has normal kidney function or CKD,
whether a subject is predisposed to developing CKD, whether CKD is
progressing in a subject, whether a subject has high stage (severe
or very severe kidney function reduction), mid-stage (moderately
reduced function) or low stage (mildly reduced function) CKD, etc.
A different exemplary mathematical model may use the measured
levels of any number of biomarkers (for example, 2, 3, 5, 7, 9,
etc.) from a subject to classify a subject based on the level or
stage of kidney function (e.g., high, moderate, low).
[0080] In one example, the identification of biomarkers for CKD
allows for the diagnosis of CKD in a subject not previously
diagnosed with CKD. For example, in a subject with risk factors for
CKD (e.g., age over 60 years, hypertension, diabetes,
cardiovascular disease, and/or a family history of CKD, etc.), the
biomarkers described herein may be used to diagnose or aid in the
diagnosis of CKD.
[0081] In another example, the identification of biomarkers for CKD
allows for early detection and diagnosis before CKD can be
diagnosed using the current standards for determining kidney
function (e.g., SCr, eGFR, urine albumin, cystatin C and/or BUN
measurements). The early diagnosis of CKD may allow earlier
therapeutic intervention which could delay or prevent the
development of further kidney damage and more severe CKD.
[0082] In another example, the biomarkers disclosed herein may be
used to diagnose or aid in diagnosing CKD in patients where the
current standards for determining CKD (e.g., SCr, urine albumin,
cystatin C, and/or BUN measurements) in subjects are inaccurate due
to, for example, chronic illness, obesity, advanced age, vegetarian
diet, and/or generally reduced muscle mass in the subject. For
example, in a subject with type 2 diabetes, the biomarkers
described herein may be used to diagnose or aid in the diagnosis of
CKD.
C. Compositions & Kits
[0083] Any of the described methods, alone or in combination, may
be performed using tools provided in the form of a kit. Kits may
further comprise appropriate controls, standards and/or detection
reagents. In an embodiment, the kit may include tools and reagents
for the analysis of a blood-based sample. The kit may comprise a
sample collection element and a vessel for storing the sample. For
example, the kit may comprise a sample collection element, a
retrieved serum collection receptacle, sample labels, sample
barcodes, and instruction protocol. The instruction protocol may be
provided as a printed form or booklet or on an electronic medium,
such as, for example, a computer disk or other computer readable
medium.
[0084] The kit may be used in accordance with the following
exemplary method. A serum sample may be collected from the subject
using a needle and syringe. The serum can then be extruded into a
collection receptacle (e.g., a vial, a conical tube, etc.). The
sample in the collection receptacle may then be subjected to
biochemical analysis. Barcodes and labels enable the sample
identity and the analyses results to be tracked through the
biochemical analysis.
[0085] The invention will be further explained with the following
examples which are offered by illustration and not limitation.
EXAMPLES
I. General Methods
A. Identification of Metabolic Profiles
[0086] Generally, each sample was analyzed to determine the
concentration of several hundred metabolites. Analytical techniques
such as GC-MS (gas chromatography-mass spectrometry) and LC-MS
(liquid chromatography-mass spectrometry) were used to analyze the
metabolites. Multiple aliquots were simultaneously, and in
parallel, analyzed, and, after appropriate quality control (QC),
the information derived from each analysis was recombined. Every
sample was characterized according to several thousand
characteristics, which ultimately amount to several hundred
chemical species. The techniques used were able to identify novel
and chemically unnamed compounds.
[0087] Samples were collected from a cohort of patients as
described in Example 1. Metabolites were extracted and proteins
were precipitated from the samples (100 .mu.l) by the addition of
450 .mu.l of methanol. Two separate UPLC methods were utilized, one
in acidic conditions and the other in basic conditions. The
precipitated extract was split into four aliquots and dried under
nitrogen and then in vacuo. One aliquot was reconstituted in 50
.mu.l of 0.1% formic acid in water (for use in the acidic method),
and another aliquot was reconstituted in 50 .mu.l of 6.5 mM
ammonium bicarbonate in water, pH 8 (for use in the basic
method).
[0088] Both methods used chromatography which was performed on 2.1
mm.times.100 mm Acquity 1.7 um C18 BEH columns (Waters Corp.,
Milford, Mass., USA) using an Acquity UPLC system. The mobile
phase, at a flow rate of 350 .mu.L/min, used solvent A, 0.1% formic
acid in water, and solvent B, 0.1% formic acid in methanol
(gradient profile: 0% B to 70% B in 4 min, 70 to 98% B in 0.5 min,
98% B for 0.9 min), for the acidic method. Sample aliquots
processed for the basic method were gradient-eluted at a flow rate
of 350 .mu.L/min using solvent A, 6.5 mM ammonium bicarbonate in
water, pH 8, and solvent B, 6.5 mM ammonium bicarbonate in 95/5
methanol/water (gradient profile: 0% B to 70% B in 4 min, 70 to 98%
B in 0.5 min, 98% B for 0.9 min).
[0089] The sample eluents were analyzed using an LTQ mass
spectrometer (MS) (ThermoFisher Corporation) using electrospray
ionization (ESI). The acidic method monitored for positive ions and
the basic method monitored for negative ions in independent
injections using separate acid/base dedicated columns heated to
40.degree. C. The MS interface capillary was maintained at
350.degree. C., with a sheath gas flow of 40 (arbitrary units) and
aux gas flow of 5 (arbitrary units) for both positive and negative
injections. The spray voltage for the positive ion injection was
4.5 kV and 3.75 kV for the negative ion injection. The instrument
scanned 99-1000 m/z and alternated between MS and MS/MS scans. The
scan speed was approximately 6 scans/sec (3 MS and 3 MS/MS scans).
MS/MS normalized collision energy was set to 40, activation Q 0.25,
and activation time 30 ms, with a 3 m/z isolation window. MS/MS
scans were collected using dynamic exclusion with an exclusion time
of 3.5 sec. Isotopically labeled compounds were spiked into every
sample and were used to assess instrument performance and
suitability, including retention time, mass and sensitivity
stability over the course of the run (usually 20 hours). In
addition, a quality control sample, which consisted of a pooled
aliquot from all samples, was analyzed every 8 injections to ensure
technical reproducibility.
[0090] Software using standard industry approaches for MS peak
detection was used for the detection and integration of MS peaks.
Briefly, extracted ion chromatograms were binned by mass in a given
range, baseline noise was determined, peak areas were calculated,
and various user-defined peak thresholds including minimum height,
signal-to-noise, width, symmetry, and area were applied to detected
MS peaks. MS peaks passing above threshold criteria were assembled
into lists that were then inserted into a relational database for
storage and further analysis. Finally, individual MS peaks were
grouped based on peak apex retention time for ease of viewing
similarly retained ion features. All samples were aligned based on
retention time (RT) markers present throughout the chromatogram
using a retention index (RI). The retention index of a sample
component is a number, obtained by interpolation (usually
logarithmic), relating the adjusted retention volume (time) or the
retention factor of the sample component to the adjusted retention
volumes (times) of two standards eluted before and after the peak
of the sample component.
[0091] The resulting data were searched against a chemical library
generated specifically for each method (e.g. UPLC positive ion data
was searched against a library specific for UPLC positive ion
mode). Biochemical identifications were based on three criteria:
retention index within 75 RI units of the proposed identification
(or approximately 5 s), experimental precursor mass match to the
library within 0.4 m/z, and the MS/MS forward and reverse scores.
The MS/MS scores were based on a comparison of the ions present in
the experimental spectrum to the ions present in the library
spectrum. Biochemical identification was performed by a software
program, and the computer generated identification was verified by
a human analyst.
[0092] Computer software checked all ions that were not assigned to
any library entry across a set of injections and within a specified
chromatographic time window. By correlating ions across multiple
injections, the natural biological variability of biochemicals was
used to identify possible new authentic biochemicals that were not
already included as an entry as part of the library. Any
biochemicals that did not have a library match but were determined
to be bona fide biochemicals based on the recurrent nature of the
spectral pattern for that biochemical were added to the library so
that the biochemical, although unnamed, could be tracked in current
and future studies. Thus, although the biochemical was not
identified (because an authentic chemical standard was not
available in the library), the properties or behavior of the
biochemical that were obtained from the analysis method were
indicated, without indicating the specific chemical composition or
structure of the biochemical (referred to as unnamed
biochemicals).
[0093] Unnamed biochemicals represent entities for which the "ion
fragmentation signature" has been established but for which no
known standard is available in the chemical library. The unnamed
biochemicals have been sufficiently characterized by analytical
techniques (described above) for unique identification. The unnamed
biochemicals are designated herein by the nomenclature "X-"
followed by a specific five digit number. Identifying analytical
information for the unnamed biochemical small molecules listed in
Table 1 is described. For example, for unnamed metabolite X-17299,
the retention time was 1.2, the retention index was 1265.9, the
quant mass was 229.2, and the polarity of the quantitative ion
using the analytical methods described above was positive as
measured on the LC-MS/MS optimized for acidic species. In an
additional example, for unnamed metabolite X-11564, the retention
time was 1.2, the retention index was 1188, the quant mass was
177.1, and the polarity of the quantitative ion using the
analytical methods described above was negative as measured on the
LC-MS/MS optimized for basic species. These analytical
characteristics allow said biomarkers (X-17299 and X-11564) to be
monitored even though an exact chemical identity (i.e., compound
name) is not known.
B. Statistical Analysis
[0094] The data were analyzed using t-tests to identify molecules
(either known, named metabolites or unnamed metabolites) present at
differential levels in a definable population or subpopulation
(e.g., biomarkers for subjects with kidney function impairment
compared to subjects without kidney function impairment) useful for
distinguishing between the definable populations (e.g., kidney
function impairment and no kidney function impairment). Other
molecules (either known, named metabolites or unnamed metabolites)
in the definable population or subpopulation were also
identified.
[0095] The data were also analyzed using correlation analysis to
identify molecules (either known, named metabolites or unnamed
metabolites) that correlate with eGFR calculations (e.g., CKD-EPI
eGFR, MDRD
[0096] Multiple regression analysis was used to evaluate the
predictive value for exemplary panels of biomarkers.
[0097] Based on the metabolite biomarker level, the sensitivity and
specificity for the classification of the samples were calculated.
Sensitivity is the ability to identify positives or the proportion
of subjects classified as positive among all those that are truly
positive. Specificity is the ability to identify negatives or the
proportion of the subjects classified as negative among all those
that are truly negative. Using these data, a receiver operating
characteristic (ROC) curve was generated. The ROC curve is a
mathematical model and is a plot of the sensitivity vs. false
positive rate (1-specificity). The area under the curve (AUC) from
this curve is the probability that a classifier will rank a
randomly chosen positive instance higher than a randomly chosen
negative one.
Example 1: Biomarkers to Assess Kidney Function
[0098] The samples used for the analysis were serum samples
collected from 281 diabetic individuals. Patient kidney function
was evaluated using two equations for estimating GFR, 1) MDRD eGFR
and 2) CKD-EPI eGFR. Using the MDRD eGFR estimates, patients with
eGFR less than 60 ml/min/1.73 m.sup.2 were classified as having
CKD, and the patients with eGFR=60 ml/min/1.73 m.sup.2 or greater
were classified as Normal. A total of 46 patients were classified
as having CKD, and 235 patients were classified as Normal at the
time of sample collection.
[0099] After the levels of metabolites were determined, the data
were analyzed using t-tests. Biomarkers for kidney function were
identified by comparing CKD vs. Normal samples. As listed in Table
1 below, the analysis resulted in the identification of biomarkers
that are differentially present between CKD and Normal patient
serum samples. All biomarkers in Table 1 are statistically
significant (p<0.1). As another way to identify biomarkers for
kidney function impairment, a correlation analysis was performed
between biomarker levels and eGFR calculations (i.e., MDRD eGFR and
CKD-EPI eGFR). The correlation value for each biomarker is shown in
Table 1.
[0100] Table 1 includes, for each biomarker, the biochemical name
of the biomarker, the correlation value of the biomarker with MDRD,
the correlation value of the biomarker with CKD-EPI, the fold
change of the biomarker in subjects with CKD compared to Normal
subjects (CKD/Normal) which is the ratio of the mean level of the
biomarker in CKD samples as compared to the Normal mean level, and
the p-value determined in the statistical analysis of the data
concerning the biomarkers. Table 1 also lists the following: the
identifier for the biomarker compound in the Kyoto Encyclopedia of
Genes and Genomes (KEGG), if available; and the identifier for the
biomarker compound in the Human Metabolome Database (HMDB), if
available.
TABLE-US-00001 TABLE 1 Biomarkers to assess kidney function
Correlation with CKD/Normal eGFR by: Fold Biochemical Name MDRD
CKD-EPI Change P-value KEGG HMDB N-acetylthreonine -0.6187 -0.6897
1.5403 p < 0.0001 C01118 erythronate -0.5298 -0.6393 1.5487 p
< 0.0001 HMDB00613 N-acetylalanine -0.5848 -0.6502 1.3258 p <
0.0001 C02847 HMDB00766 arabitol -0.5153 -0.6022 2.0099 p <
0.0001 C00474 HMDB01851 N-acetylserine -0.6004 -0.6736 1.6718 p
< 0.0001 HMDB02931 myo-inositol -0.544 -0.6216 1.7167 p <
0.0001 C00137 HMDB00211 kynurenine -0.4968 -0.5619 1.3355 p <
0.0001 C00328 HMDB00684 trans-4-hydroxyproline -0.1227 -0.1345
1.1241 0.135235 C01157 HMDB00725 tryptophan 0.2418 0.2986 0.8968
0.0002 C00078 HMDB00929 3-methylhistidine -0.224 -0.2979 1.8903
0.0017 C01152 HMDB00479 4-acetamidobutanoate -0.5563 -0.6526 1.5779
p < 0.0001 C02946 HMDB03681 N6- -0.584 -0.6704 1.6955 p <
0.0001 carbamoylthreonyladenosine erythritol -0.5563 -0.6362 1.9232
p < 0.0001 C00503 HMDB02994 3-methylglutarylcarnitine -0.5013
-0.5784 2.5612 p < 0.0001 HMDB00552 (C6) S-adenosylhomocysteine
-0.501 -0.5799 1.5955 p < 0.0001 C00021 HMDB00939 (SAH)
N1-methyladenosine -0.502 -0.5713 1.2493 p < 0.0001 C02494
HMDB03331 N2,N2-dimethylguanosine -0.5047 -0.5656 1.4345 p <
0.0001 HMDB04824 N-acetylcarnosine -0.4513 -0.4846 1.5465 p <
0.0001 arabonate -0.4849 -0.562 1.949 p < 0.0001 HMDB00539
p-cresol sulfate -0.3864 -0.4835 1.92 p < 0.0001 C01468
HMDB11635 xylonate -0.461 -0.5561 1.775 p < 0.0001 C05411
N-formylmethionine -0.4554 -0.5439 1.382 p < 0.0001 C03145
HMDB01015 succinylcarnitine -0.4716 -0.5435 1.6696 p < 0.0001
O-methylcatechol sulfate -0.4525 -0.5431 2.1496 p < 0.0001
N-acetylmethionine -0.5005 -0.5381 1.5394 p < 0.0001 C02712
HMDB11745 N2,N5-diacetylornithine -0.4462 -0.5328 1.9997 p <
0.0001 ribose -0.4688 -0.5324 2.1962 p < 0.0001 C00121 HMDB00283
2-methylbutyrylcarnitine -0.4514 -0.5212 1.7446 p < 0.0001
HMDB00378 (C5) N4-acetylcytidine -0.4512 -0.4937 1.5599 p <
0.0001 HMDB05923 N1-Methyl-2-pyridone-5- -0.4459 -0.4919 1.6845 p
< 0.0001 C05842 HMDB04193 carboxamide 1-methylhistidine -0.423
-0.4809 2.1189 0.0006 C01152 HMDB00001 pyroglutamine -0.4327
-0.4782 1.629 p < 0.0001 tiglyl carnitine -0.4342 -0.4762 1.483
0.0001 HMDB02366 5-methylthioadenosine -0.3689 -0.4654 1.7931 p
< 0.0001 C00170 HMDB01173 (MTA) isobutyrylcarnitine -0.3896
-0.4634 1.9746 p < 0.0001 HMDB00736 indolelactate -0.3987
-0.4565 1.434 0.0002 C02043 HMDB00671 glutarylcarnitine (C5)
-0.4069 -0.447 1.4393 p < 0.0001 HMDB13130 choline -0.3417
-0.4423 1.2088 p < 0.0001 C00114 1-methylurate -0.3759 -0.4346
1.5167 p < 0.0001 HMDB03099 hydroxyisovaleroyl carnitine -0.3817
-0.4264 1.668 p < 0.0001 pro-hydroxy-pro -0.376 -0.4263 1.7757
0.0006 HMDB06695 N-acetyl-3-methylhistidine -0.3329 -0.4102 1.7492
0.0067 salicyluric glucuronide -0.3123 -0.4062 4.578 0.0036
scyllo-inositol -0.3506 -0.3965 1.5525 0.0013 C06153 HMDB06088
quinate -0.3438 -0.3928 1.922 0.0021 C00296 HMDB03072
2,3-dihydroxyisovalerate -0.3285 -0.375 2.5621 0.0036 C04039
trigonelline (N'- -0.3246 -0.3691 1.7038 p < 0.0001 C01004
HMDB00875 methylnicotinate) propionylcarnitine -0.3266 -0.3629
1.3841 0.0001 C03017 HMDB00824 3-methylxanthine -0.3153 -0.3558
1.66 0.0051 C16357 HMDB01886 1,3,7-trimethylurate -0.3243 -0.3426
1.901 0.0041 C16361 HMDB02123 tartarate -0.2925 -0.3371 2.7353
0.0088 C00898 HMDB00956 phenylcarnitine -0.2847 -0.3328 2.1264
0.0358 N-acetylphenylalanine -0.2945 -0.3318 1.381 0.0002 C03519
HMDB00512 3-methyl catechol sulfate 1 -0.3161 -0.3304 1.7389 0.0018
4-hydroxyphenylacetate -0.264 -0.3282 1.816 0.0306 C00642 HMDB00020
cystine -0.2673 -0.3209 1.9586 0.0245 C00491 HMDB00192
acetylcarnitine -0.2831 -0.3159 1.1845 0.0014 C02571 HMDB00201
guanosine -0.2982 -0.3139 1.537 p < 0.0001 C00387 HMDB00133
furosemide -0.2481 -0.3057 2.0624 0.0185 D00331 HMDB01933 xanthine
-0.2493 -0.2949 1.9277 0.0425 C00385 HMDB00292 4-acetylphenol
sulfate -0.297 -0.285 1.9232 0.0012 C00548 cis-4-decenoyl carnitine
-0.2656 -0.2831 1.3248 0.0028 phenyllactate (PLA) -0.2415 -0.2804
1.5813 0.0447 C05607 HMDB00779 stachydrine -0.219 -0.2628 1.6889
0.0059 C10172 HMDB04827 N-delta-acetylornithine -0.1927 -0.2494
1.7173 0.0004 5-acetylamino-6- -0.2297 -0.2439 2.4545 0.0179 C16365
HMDB11105 formylamino-3-methyluracil 2-aminophenol sulfate -0.2355
-0.2414 1.6228 0.0005 chiro-inositol -0.1817 -0.2405 2.2202 0.0266
mannitol -0.1836 -0.2397 3.0328 0.018 C00392 HMDB00765
taurocholenate sulfate -0.199 -0.2297 1.9086 0.014
hydrochlorothiazide -0.1787 -0.2196 2.1933 0.0336 C07041 HMDB01928
1-linoleoylglycerol (1- -0.1768 -0.1966 1.5333 0.0016 monolinolein)
histidylphenylalanine -0.0172 -0.0069 0.3352 0.0317
ADSGEGDFXAEGGGVR 0.0259 0.0269 0.3517 0.0181 HXGXA 0.0716 0.1187
0.3912 0.002 stearoyl sphingomyelin 0.123 0.1254 0.8587 0.002
C00550 HMDB01348 3-methyl-2-oxovalerate 0.1222 0.142 0.9061
0.0553776 C00671 HMDB03736 oleamide 0.2356 0.1621 0.1499 p <
0.0001 HMDB02117 4-methyl-2-oxopentanoate 0.1603 0.1732 0.9022
0.0474 C00233 HMDB00695 3-methyl-2-oxobutyrate 0.1499 0.1955 0.9085
0.0087 C00141 HMDB00019 lathosterol 0.1904 0.2377 0.7393 0.0024
C01189 HMDB01170 glycerophosphorylcholine 0.3754 0.3384 0.6102 p
< 0.0001 C00670 HMDB00086 (GPC) indoleacetylglutamine -0.183
-0.22 1.6285 0.0023 palmitoyl sphingomyelin 0.1465 0.1794 0.8685
0.0001 urea -0.5269 -0.5702 1.4498 p < 0.0001 C00086 HMDB00294
X-11564 -0.6573 -0.5961 1.0487 0.390639 X-17299 -0.6484 -0.582
1.1898 0.012403 pseudouridine -0.6659 -0.7484 1.6032 p < 0.0001
C02067 HMDB00767 C-glycosyltryptophan -0.6017 -0.6928 1.6913 p <
0.0001 creatinine -0.6322 -0.6732 1.4077 p < 0.0001 C00791
HMDB00562 N6-acetyllysine -0.4973 -0.5513 1.368 p < 0.0001
C02727 HMDB00206 phenylacetylglutamine -0.4481 -0.5484 2.2309 p
< 0.0001 C04148 HMDB06344 threitol -0.4189 -0.4883 1.9801 p <
0.0001 C16884 HMDB04136 3-indoxyl sulfate -0.3875 -0.4422 1.4877 p
< 0.0001 HMDB00682 2-hydroxyhippurate -0.1561 -0.2047 5.3527
0.0145 C07588 HMDB00840 (salicylurate)
Example 2: Diagnostic Performance of Individual Biomarkers for
Kidney Function Assessment
[0101] In another example, three exemplary biomarkers to assess
kidney function and identify individuals with CKD were selected
from Table 1 and evaluated for diagnostic performance. These models
are intended to be non-limiting and are presented to exemplify the
invention. The biomarkers identified were present at levels that
differed between patient samples from individuals with normal
kidney function and samples from individuals with CKD. For example,
C-glycosyltryptophan, N-acetylthreonine, and pseudouridine were
significant biomarkers for distinguishing subjects with CKD from
normal subjects.
[0102] The samples used for the analysis were serum samples
collected from 281 diabetic individuals. Patient kidney function
was evaluated using the MDRD equation to estimate GFR. Patients
with MDRD eGFR values of less than 60 ml/min/1.73 m.sup.2 were
classified as having CKD, and patients with eGFR values of 60
ml/min/1.73 m.sup.2 or greater were classified as Normal. A total
of 46 patients were classified as having CKD, and 235 patients were
classified as Normal at the time of sample collection. The
biomarkers identified in Example 1, Table 1, for diagnosing or
aiding in the diagnosis of CKD were evaluated for diagnostic
performance using Receiver Operator Characteristic (ROC) curve
modeling.
[0103] The exemplary biomarker C-glycosyltryptophan was evaluated
for diagnostic performance. FIG. 3A shows the distribution of
patient samples based on the level of C-glycosyltryptophan measured
in the samples. The x-axis shows the diagnosis group (Normal or
CKD), and the y-axis shows the level of C-glycosyltryptophan. Next,
the levels of C-glycosyltryptophan were used in a mathematical
model to determine the diagnostic performance of the biomarker.
FIG. 3B shows the ROC curve for C-glycosyltryptophan. The ROC curve
has an area under the curve (AUC) of 0.8721. Based on this ROC
curve, it was determined that by measuring the level of
C-glycosyltryptophan, CKD subjects were distinguished from Normal
subjects with 85% sensitivity and 80% specificity.
[0104] The exemplary biomarker N-acetylthreonine was also evaluated
for diagnostic performance. FIG. 4A shows the distribution of
patient samples based on the level of N-acetylthreonine measured in
the samples. The x-axis shows the diagnosis group (Normal or CKD),
and the y-axis shows the level of N-acetylthreonine. Next, the
levels of N-acetylthreonine were used in a mathematical model to
determine the diagnostic performance of the biomarker. FIG. 4B
shows the ROC curve for N-acetylthreonine. The ROC curve has an AUC
of 0.8801. Based on this ROC curve it was determined that by
measuring the level of N-acetylthreonine, CKD subjects were
distinguished from normal subjects with 83% sensitivity and 87%
specificity.
[0105] The exemplary biomarker pseudouridine was also evaluated for
diagnostic performance. FIG. 5A shows the distribution of patient
samples based on the level of pseudouridine measured in the
samples. The x-axis shows the diagnosis group (Normal or CKD), and
the y-axis shows the level of pseudouridine. Next, the levels of
pseudouridine were used in a mathematical model to determine the
diagnostic performance of the biomarker. FIG. 5B shows the ROC
curve for pseudouridine. The ROC curve has an AUC of 0.9041. Based
on this ROC curve it was determined that by measuring the level of
pseudouridine, CKD subjects were distinguished from Normal subjects
with 80% sensitivity and 93% specificity.
Example 3: Diagnostic Performance of Panels of Biomarkers for
Kidney Function Assessment
[0106] In another example, mathematical models that provide an
estimation of GFR were developed. These model GFR estimations were
used to evaluate kidney function, and the performance of the
estimations obtained using these models were compared to the eGFR
calculated using the CKD-EPI equation ("CKD-EPI eGFR"). Five
exemplary models were developed using combinations of the following
biomarkers: pseudouridine, N-acetylthreonine, C-glycosyltryptophan,
kynurenine, myo-inositol, creatinine. The exemplary biomarkers are
also described in Example 1 as significant for distinguishing
individuals with normal kidney function from those with CKD. These
models are intended to be non-limiting and are presented to
exemplify the invention.
[0107] The biomarkers pseudouridine, N-acetylthreonine,
C-glycosyltryptophan, kynurenine, myo-inositol, and creatinine were
measured in fasting serum samples collected from 258 diabetic
individuals for whom the CKD-EPI equation to estimate GFR was used
to evaluate kidney function. Patients with CKD-EPI eGFR values of
60 ml/min/1.73 m.sup.2 or less were classified as having a
"positive" diagnosis (i.e., compromised kidney function, CKD), and
patients with eGFR values of greater than 60 ml/min/1.73 m.sup.2
were classified as having a "negative" (i.e., normal kidney
function). A total of 40 patients were classified as a positive
diagnosis for CKD and/or compromised kidney function, and 218
patients were classified as a negative diagnosis and/or normal
kidney function based on CKD-EPI eGFR results.
[0108] In the present example, five models were generated using
multiple regression analysis: exemplary Model 1 comprises the
biomarkers pseudouridine, C-glycosyltryptophan, N-acetylthreonine,
and creatinine; exemplary Model 2 comprises the biomarkers
pseudouridine, N-acetylthreonine, myo-inositol, and creatinine;
exemplary Model 3 comprises the biomarkers N-acetylthreonine,
myo-inositol, C-glycosyltryptophan, and creatinine; exemplary Model
4 comprises the biomarkers N-acetylthreonine, myo-inositol,
kynurenine, and creatinine; and exemplary Model 5 comprises the
biomarkers pseudouridine, C-glycosyltryptophan, N-acetylthreonine,
and myo-inositol. Each model was evaluated for its diagnostic
performance using Receiver Operating Characteristic (ROC) and by
calculating the area under the curve (AUC).
[0109] For exemplary Model 1, the GFR values calculated using Model
1 were significantly correlated with the values calculated using
the CKD-EPI eGFR; the adjusted R.sup.2 was 0.614 with an overall
p-value of less than 0.001. The diagnostic performance of Model 1
based on the calculated AUC was 0.932. The results of the
correlation analysis for Model 1 are displayed graphically in FIG.
6A. The GFR calculated using Model 1 is plotted on the x-axis, and
the CKD-EPI eGFR is plotted on the y-axis.
[0110] For exemplary Model 2, the GFR values calculated using Model
2 were correlated with the values calculated using the CKD-EPI
eGFR; the adjusted R.sup.2 was 0.614 with an overall p-value of
less than 0.0001. The diagnostic performance of Model 2 based on
the calculated AUC was 0.932. The results of the correlation
analysis for Model 2 are displayed graphically in FIG. 6B. The GFR
calculated using Model 2 is plotted on the x-axis, and the CKD-EPI
eGFR is plotted on the y-axis.
[0111] For exemplary Model 3, the GFR values calculated using Model
3 were correlated with the values calculated using the CKD-EPI
eGFR; the adjusted R.sup.2 was 0.594 with an overall p-value of
less than 0.0001. The diagnostic performance of Model 3 based on
the calculated AUC was 0.931. The results of the correlation
analysis for Model 3 are displayed graphically in FIG. 6C. The GFR
calculated using Model 3 is plotted in the x-axis, and the CKD-EPI
eGFR is plotted on the y-axis.
[0112] For exemplary Model 4, the GFR values calculated using Model
4 were significantly correlated with the values calculated using
the CKD-EPI eGFR; the adjusted R.sup.2 was 0.613 with an overall
p-value of less than 0.0001. The diagnostic performance of Model 4
based on the calculated AUC was 0.935. The results of the
correlation analysis for Model 4 are displayed graphically in FIG.
6D. The GFR calculated using Model 4 is plotted on the x-axis, and
the CKD-EPI eGFR is plotted on the y-axis.
[0113] For exemplary Model 5, the GFR values calculated using Model
5 were significantly correlated with the values calculated using
the CKD-EPI eGFR; the adjusted R.sup.2 was 0.563 with an overall
p-value of less than 0.0001. The diagnostic performance of Model 5
based on the calculated AUC was 0.933. The results of the
correlation analysis for Model 5 are displayed graphically in FIG.
6E. The GFR calculated using Model 5 is plotted on the x-axis, and
the CKD-EPI eGFR is plotted on the y-axis.
Example 4: Biomarkers to Assess Kidney Function in Patients with
Intermediate
[0114] eGFR
[0115] For patients with eGFR in an intermediate (G2-G3a) range
with eGFR between 45 and 74 mL/min per 1.63 m.sup.2 and/or
intermediate urine albumin scores, the assessment of kidney
function and diagnosis of CKD is uncertain; such patients would
benefit from a more precisely estimated GFR such as a metabolite
biomarker test. The integration of such a novel biomarker test into
a kidney function assessment and treatment algorithm is illustrated
in FIG. 1.
[0116] Biomarkers useful for evaluating kidney function and
estimating GFR were identified by measuring the level of the
biomarkers in serum samples and urine samples from diabetic
individuals with eGFR values of 40-80.
[0117] Serum samples from 78 individuals for whom the MDRD eGFR and
69 individuals for whom the CKD-EPI eGFR values fell in this range
were analyzed. The levels of the biomarkers were correlated with
the MDRD eGFR and the CKD-EPI eGFR values. The results of the
correlations are presented in Table 2. For each biomarker listed in
Table 2 the biochemical name of the biomarker, the correlation
value of the biomarker with CKD-EPI eGFR, the p-value of the
correlation of the biomarker with CKD-EPI eGFR, the correlation
value of the biomarker with MDRD eGFR, and the p-value of the
correlation of the biomarker with MDRD eGFR are displayed.
TABLE-US-00002 TABLE 2 Serum biomarkers for assessing kidney
function in patients with eGFR of 40-80 CKD-EPI eGFR (Serum) MDRD
eGFR (Serum) Biomarker Name Correlation p-value Correlation p-value
pseudouridine -0.6412 2.93E-09 -0.6016 5.71E-09 N-acetylthreonine
-0.5323 2.51E-06 -0.5267 7.31E-07 C-glycosyltryptophan -0.5614
5.20E-07 -0.5153 1.39E-06 X-11564 -0.5685 3.47E-07 -0.5206 1.03E-06
N6-carbamoylthreonyladenosine -0.5656 4.11E-07 -0.5055 2.35E-06
N4-acetylcytidine -0.5451 1.28E-06 -0.5687 5.58E-08
N1-Methyl-2-pyridone-5-carboxamide -0.524 3.83E-06 -0.4698 1.43E-05
urea -0.5096 7.74E-06 -0.5015 2.91E-06 X-17299 -0.501 1.16E-05
-0.4468 4.11E-05 N-acetylserine -0.4931 1.67E-05 -0.4459 4.29E-05
4-acetamidobutanoate -0.4909 1.85E-05 -0.4185 0.0001
N-acetylalanine -0.4803 2.96E-05 -0.4185 0.0001 creatinine -0.4749
3.74E-05 -0.4163 0.0002 5-methylthioadenosine (MTA) -0.4518
9.74E-05 -0.4319 7.86E-05 glycerophosphorylcholine (GPC) 0.4456
0.0001 0.4796 8.89E-06 ribose -0.4224 0.0003 -0.4328 7.57E-05
N1-methyladenosine -0.4171 0.0004 -0.3644 0.001
phenylacetylglutamine -0.4137 0.0004 -0.3799 0.0006 pro-hydroxy-pro
-0.4122 0.0004 -0.415 0.0002 propionylcarnitine -0.4109 0.0005
-0.4319 7.86E-05 2-methylbutyrylcarnitine (C5) -0.4049 0.0006
-0.3792 0.0006 guanosine -0.4043 0.0006 -0.3719 0.0008
succinylcarnitine -0.3993 0.0007 -0.3941 0.0004 erythronate -0.396
0.0008 -0.3974 0.0003 kynurenine -0.3941 0.0008 -0.31 0.0058
N6-acetyllysine -0.3908 0.0009 -0.3466 0.0019 choline -0.3819
0.0012 -0.2876 0.0107 isobutyrylcarnitine -0.381 0.0012 -0.3827
0.0005 tryptophan 0.3738 0.0016 0.2994 0.0077 myo-inositol -0.3725
0.0016 -0.3579 0.0013 gamma-glutamylphenylalanine -0.3716 0.0017
-0.3651 0.001 phenylcarnitine -0.3711 0.0017 -0.3876 0.0005
palmitoyl sphingomyelin 0.3695 0.0018 0.3686 0.0009 salicyluric
glucuronide -0.3689 0.0018 -0.3126 0.0053 glutarylcarnitine (C5)
-0.367 0.0019 -0.3391 0.0024 S-adenosylhomocysteine (SAH) -0.3619
0.0022 -0.3438 0.0021 furosemide -0.3589 0.0025 -0.3332 0.0029
1-methylhistidine -0.3576 0.0026 -0.3374 0.0025
2-hydroxyisobutyrate -0.3555 0.0027 -0.3352 0.0027 p-cresol sulfate
-0.3531 0.0029 -0.3042 0.0068 2-hydroxyhippurate (salicylurate)
-0.3472 0.0035 -0.3223 0.004 chiro-inositol -0.3456 0.0036 -0.3141
0.0051 deoxycarnitine -0.3419 0.004 -0.287 0.0108 O-methylcatechol
sulfate -0.3405 0.0042 -0.3567 0.0013 hydroxyisovaleroyl carnitine
-0.3384 0.0045 -0.3166 0.0047 N-delta-acetylornithine -0.3322
0.0053 -0.398 0.0003 N2,N2-dimethylguanosine -0.3264 0.0062 -0.2851
0.0114 xylonate -0.3244 0.0065 -0.2949 0.0088
3-methylglutarylcarnitine (C6) -0.321 0.0072 -0.2833 0.012
gamma-glutamylvaline -0.3172 0.0079 -0.3666 0.001 kynurenate
-0.3147 0.0084 -0.2818 0.0124 1- -0.3057 0.0106 -0.3231 0.0039
pentadecanoylglycerophosphocholine arabitol -0.3052 0.0108 -0.3268
0.0035 stachydrine -0.3045 0.011 -0.2543 0.0247
gamma-glutamylmethionine -0.3004 0.0122 -0.3254 0.0036 cystine
-0.2994 0.0125 -0.2351 0.0383 fucose -0.2906 0.0154 -0.3022 0.0072
3-indoxyl sulfate -0.282 0.0189 -0.273 0.0156 threitol -0.2765
0.0214 -0.2583 0.0224 1-linoleoylglycerol (1-monolinolein) -0.2756
0.0219 -0.2561 0.0236 erythritol -0.2748 0.0223 -0.2691 0.0172
N2,N5-diacetylornithine -0.2673 0.0264 -0.2862 0.0111
N-formylmethionine -0.264 0.0284 -0.2501 0.0272 N-acetylcarnosine
-0.2624 0.0294 -0.184 0.1069 1-oleoylglycerol (1-monoolein) -0.2607
0.0305 -0.2573 0.0229 pantothenate -0.2584 0.032 -0.2597 0.0217
gamma-glutamylglutamine -0.2546 0.0347 -0.2871 0.0108 arabonate
-0.2527 0.0362 -0.2683 0.0176 gamma-glutamylleucine -0.2454 0.0421
-0.282 0.0124 tiglyl carnitine -0.2428 0.0444 -0.2551 0.0242
cysteine -0.2425 0.0447 -0.2447 0.0308 gamma-glutamyltyrosine
-0.2367 0.0502 -0.2293 0.0434 2-aminophenol sulfate -0.2326 0.0545
-0.2402 0.0341 5-acetylamino-6-formylamino-3- -0.2297 0.0576
-0.2185 0.0546 methyluracil ranitidine -0.228 0.0595 -0.213 0.0611
salicylate -0.2224 0.0662 -0.1921 0.092 hippurate -0.221 0.068
-0.2139 0.06 catechol sulfate -0.2164 0.0741 -0.2564 0.0234
N-acetylaspartate (NAA) -0.2128 0.0791 -0.1664 0.1455 mannitol
-0.2122 0.08 -0.1826 0.1096 indolelactate -0.2054 0.0905 -0.1898
0.096 N-acetyl-3-methylhistidine -0.2051 0.091 -0.188 0.0992
gamma-glutamylisoleucine -0.2039 0.0929 -0.2494 0.0276 phenol
sulfate -0.2002 0.0991 -0.1723 0.1314 gluconate -0.1984 0.1022
-0.2148 0.059 trigonelline (N'-methylnicotinate) -0.1846 0.1289
-0.2241 0.0486 HWESASLLR -0.1778 0.1438 -0.2589 0.0221
N-acetylmethionine -0.1731 0.155 -0.206 0.0703 acetylcarnitine
-0.1603 0.1883 -0.2195 0.0535 bilirubin (E,E) 0.1558 0.2011 0.2033
0.0743 theophylline 0.1624 0.1825 0.2186 0.0545 pregnen-diol
disulfate 0.1662 0.1722 0.2034 0.0741 4-androsten-3beta,17beta-diol
0.1689 0.1652 0.2002 0.0789 disulfate 1 oleamide 0.1733 0.1544
0.2273 0.0453 azelate (nonanedioate) 0.1754 0.1494 0.2011 0.0775
dehydroisoandrosterone sulfate 0.1913 0.1153 0.2143 0.0596 (DHEA-S)
1-palmitoylplasmenylethanolamine 0.194 0.1101 0.214 0.0599 1-
0.2017 0.0964 0.1173 0.3063 linoleoylglycerophosphoethanolamine
3-methyl-2-oxovalerate 0.2026 0.095 0.1736 0.1284 10-undecenoate
(11:1n1) 0.2033 0.0938 0.1418 0.2157 8-aminocaprylate 0.2069 0.088
-0.0025 0.9824 1-arachidonoylglycerophosphocholine 0.2081 0.0861
0.1601 0.1615 glutamine 0.21 0.0833 0.2145 0.0594
leucylphenylalanine 0.2105 0.0825 0.1874 0.1004 cholesterol 0.2152
0.0758 0.1885 0.0983 3-ethylphenylsulfate 0.2296 0.0577 0.1378
0.2289 iminodiacetate (IDA) 0.2313 0.0558 0.1771 0.1209 cotinine
N-oxide 0.232 0.0551 0.136 0.2351 glycerol 0.233 0.0541 0.1679
0.1418 3-phosphoglycerate 0.2362 0.0507 0.1999 0.0792 campesterol
0.2369 0.0501 0.1938 0.0891 glycerol 2-phosphate 0.2438 0.0435
0.2105 0.0644 palmitate, methyl ester 0.2446 0.0428 0.1984 0.0817
octadecanedioate 0.2446 0.0428 0.2531 0.0254 2-aminooctanoate
0.2453 0.0422 0.2291 0.0436 1-linoleoylglycerophosphocholine 0.2466
0.0411 0.1776 0.1199 phosphate 0.2481 0.0399 0.2361 0.0374
pregnenolone sulfate 0.2543 0.035 0.2531 0.0253 glycerol
3-phosphate (G3P) 0.2547 0.0347 0.2504 0.027
2-linoleoylglycerophosphocholine 0.2611 0.0302 0.2151 0.0586
glycerate 0.2647 0.028 0.2837 0.0118 sebacate (decanedioate) 0.2733
0.0231 0.3051 0.0066 isoleucylleucine 0.2735 0.023 0.2405 0.0339
EDTA 0.2759 0.0218 0.2173 0.056 beta-sitosterol 0.2791 0.0202
0.2697 0.017 pyrophosphate (PPi) 0.2804 0.0196 0.2215 0.0513 pregn
steroid monosulfate 0.283 0.0185 0.2907 0.0098 eicosanodioate
0.2836 0.0182 0.237 0.0367 ethyl glucuronide 0.2904 0.0155 0.2254
0.0472 2-hydroxyoctanoate 0.2987 0.0127 0.2656 0.0187 stearoyl
sphingomyelin 0.307 0.0103 0.3483 0.0018 pyruvate 0.3092 0.0097
0.2754 0.0147 8-hydroxyoctanoate 0.3287 0.0058 0.3082 0.0061
heptanoate (7:0) 0.3308 0.0055 0.3516 0.0016 adenosine
5'-monophosphate (AMP) 0.3325 0.0053 0.3649 0.001 caproate (6:0)
0.3366 0.0047 0.3867 0.0005
[0118] Similarly, urine samples from 76 individuals for whom MDRD
eGFR and 64 individuals for whom CKD-EPI eGFR values were in this
range were analyzed. The measured levels of the biomarkers were
correlated with MDRD eGFR and CKD-EPI eGFR values. The results of
the correlations are presented in Table 3. For each biomarker, the
biochemical name of the biomarker, the correlation value of the
biomarker with CKD-EPI eGFR, the p-value of the correlation of the
biomarker with CKD-EPI eGFR, the correlation value of the biomarker
with MDRD eGFR, and the p-value of the correlation of the biomarker
with MDRD eGFR is presented.
TABLE-US-00003 TABLE 3 Urine biomarkers to assess kidney function
in patients with eGFR of 40-80 CKD-EPI eGFR (Urine) MDRD eGFR
(Urine) Biochemical Name Correlation p-value Correlation p-value
furosemide -0.3835 0.0018 -0.3193 0.0049 myo-inositol -0.3693
0.0027 -0.3493 0.002 chiro-inositol -0.3255 0.0087 -0.2936 0.01
lactose -0.2919 0.0192 -0.269 0.0188 quinolinate -0.2729 0.0291
-0.2023 0.0796 homostachydrine -0.2711 0.0302 -0.1346 0.2464
imidazole propionate -0.2624 0.0362 -0.1842 0.1111
guanidinosuccinate -0.2498 0.0465 -0.2972 0.0091
2-oxo-1-pyrrolidinepropionate -0.2451 0.0509 -0.257 0.025
N-acetylphenylalanine -0.2384 0.0578 -0.2052 0.0754
N1-Methyl-2-pyridone-5-carboxamide -0.2339 0.0629 -0.1986 0.0855
stachydrine -0.2335 0.0633 -0.1122 0.3345 N4-acetylcytidine -0.2327
0.0642 -0.1837 0.1122 N-acetyltryptophan -0.2305 0.0669 -0.2546
0.0264 ofloxacin -0.2297 0.0679 -0.2365 0.0397 5-oxoproline -0.2254
0.0733 -0.0409 0.7258 1,3,7-trimethylurate -0.2203 0.0802 -0.106
0.362 isosorbide -0.218 0.0835 -0.1914 0.0976 hydroquinone sulfate
-0.2177 0.084 -0.2127 0.0651 5-methyltetrahydrofolate (5MeTHF)
-0.2145 0.0888 -0.2145 0.0628 hydantoin-5-propionic acid -0.2116
0.0933 -0.2143 0.063 mannitol -0.2107 0.0947 -0.1993 0.0844
nicotinate -0.2039 0.1061 -0.1992 0.0845 abscisate -0.2028 0.108
-0.1704 0.1412 pipecolate -0.2026 0.1083 -0.2191 0.0572
N-acetyltyrosine -0.1898 0.133 -0.1349 0.2452 N-(2-furoyl)glycine
-0.1871 0.1388 -0.1657 0.1525 1,7-dimethylurate -0.187 0.139
-0.1136 0.3284 kynurenine -0.1794 0.1561 -0.1828 0.114 alpha-CEHC
glucuronide -0.1764 0.1632 -0.1362 0.2406 guanidine -0.173 0.1716
-0.2664 0.02 O-methylcatechol sulfate -0.1677 0.1853 -0.1881 0.1037
orotidine -0.1676 0.1856 -0.1075 0.3552 3-methoxytyrosine -0.1674
0.1862 -0.1364 0.2401 neopterin -0.1673 0.1863 -0.1842 0.1112
alanylleucine -0.1573 0.2144 -0.1742 0.1323 3-dehydrocarnitine
-0.1541 0.224 -0.1272 0.2736 phenylcarnitine -0.1494 0.2388 -0.1504
0.1947 caffeine -0.1464 0.2485 -0.1437 0.2155 orotate -0.1425
0.2614 -0.0994 0.3932 arginylisoleucine -0.141 0.2663 -0.1034
0.3743 N-acetyl-aspartyl-glutamate (NAAG) 0.1428 0.2605 0.0904
0.4373 hypoxanthine 0.1436 0.2576 0.0962 0.4084 3-methylcytidine
0.1437 0.2574 0.1196 0.3033 N-acetylglycine 0.1461 0.2494 0.0563
0.6292 mandelate 0.1473 0.2454 0.0434 0.7094 androsterone sulfate
0.1484 0.2419 0.1093 0.3472 2,3-dihydroxyisovalerate 0.1489 0.2404
0.0527 0.651 taurine 0.149 0.24 0.0706 0.5442
dehydroisoandrosterone sulfate 0.1494 0.2387 0.1481 0.2018 (DHEA-S)
N-acetylthreonine 0.15 0.2369 0.0387 0.7401 itaconate
(methylenesuccinate) 0.1503 0.2358 0.0151 0.8971 homoveratric acid
0.1522 0.2299 0.1318 0.2564 verapamil 0.1522 0.2299 0.2047 0.0761
1-methylhistidine 0.1544 0.2233 0.0946 0.4161 3-hydroxybutyrate
(BHBA) 0.1557 0.2192 0.0518 0.6568 alanine 0.1557 0.2191 0.098
0.3999 pantothenate 0.1563 0.2173 0.1216 0.2953 methyl
indole-3-acetate 0.1571 0.2151 0.0894 0.4422 N2-acetyllysine 0.1625
0.1996 0.286 0.0123 4-acetaminophen sulfate 0.1634 0.197 0.1829
0.1138 cis-aconitate 0.1638 0.196 0.0496 0.6706 5-hydroxyhexanoate
0.1639 0.1957 0.0866 0.4569 allo-threonine 0.1646 0.1936 0.0796
0.4945 2-hydroxybutyrate (AHB) 0.1647 0.1933 0.062 0.5947
homocitrate 0.1649 0.1928 0.106 0.362 acisoga 0.1651 0.1924 0.141
0.2243 arabinose 0.1667 0.188 0.0469 0.6874 lactate 0.1682 0.184
0.0733 0.5292 gentisate 0.1701 0.1791 0.0824 0.4792
N-acetylhistidine 0.1707 0.1775 0.1738 0.1332 gamma-glutamylvaline
0.1732 0.1712 0.1248 0.2828 beta-hydroxyisovalerate 0.1747 0.1674
0.0821 0.481 N-acetylproline 0.1757 0.1649 0.0402 0.7303
7-methylguanine 0.1761 0.164 0.1013 0.3839 arabitol 0.177 0.1618
0.0695 0.551 cortisol 0.1777 0.1601 0.1648 0.1547
4-methyl-2-oxopentanoate 0.1778 0.1598 0.0846 0.4673 putrescine
0.1788 0.1575 0.0585 0.6156 2-isopropylmalate 0.1789 0.1572 0.0691
0.5533 trans-urocanate 0.1803 0.154 0.1788 0.1222 tyrosine 0.1803
0.154 0.1657 0.1526 andro steroid monosulfate 2 0.1818 0.1505
0.1449 0.2117 sulforaphane 0.182 0.15 0.1276 0.272 glycine 0.1827
0.1484 0.2002 0.0829 4-androsten-3beta,17beta-diol 0.1897 0.1332
0.1766 0.1271 disulfate 1 7-ketodeoxycholate 0.1899 0.1328 0.2549
0.0263 3-ureidopropionate 0.1935 0.1255 0.1318 0.2563
3-methylglutaconate 0.1936 0.1252 0.0987 0.3963 cotinine 0.1968
0.119 0.0939 0.4197 tartarate 0.1973 0.1182 0.0788 0.4984
ethanolamine 0.2005 0.1122 0.2327 0.0431 N1-methylguanosine 0.2015
0.1103 0.2281 0.0475 succinimide 0.2036 0.1066 0.0815 0.4839 malate
0.2083 0.0986 0.0894 0.4423 3-hydroxyglutarate 0.209 0.0974 0.1233
0.2884 3-(3-hydroxyphenyl)propionate 0.2093 0.097 0.142 0.221
2-piperidinone 0.213 0.0911 0.1119 0.3359 3-hydroxyisobutyrate
0.214 0.0895 0.1118 0.3365 ibuprofen acyl glucuronide 0.2147 0.0885
0.1785 0.1229 pregnanediol-3-glucuronide 0.2163 0.086 0.0902 0.4384
lysine 0.2171 0.0848 0.2017 0.0806 adipate 0.2196 0.0813 0.1126
0.3326 3-methylglutarate 0.2197 0.0811 0.1089 0.3489
tetrahydrocortisone 0.2207 0.0797 0.1809 0.1178 prolylglycine
0.2215 0.0786 0.102 0.3808 o-cresol sulfate 0.223 0.0765 0.1157
0.3196 5alpha-pregnan-3beta,20alpha-diol 0.224 0.0751 0.1073 0.3564
disulfate histidine 0.2267 0.0716 0.1705 0.1408
3-ethylphenylsulfate 0.2278 0.0703 0.1169 0.3145
gamma-glutamylisoleucine 0.2295 0.0681 0.1393 0.23 andro steroid
monosulfate 1 0.2305 0.0669 0.1617 0.163 citramalate 0.2393 0.0568
0.0874 0.4526 2-hydroxyglutarate 0.2467 0.0494 0.1025 0.3782
3-hydroxy-3-methylglutarate 0.2474 0.0488 0.1151 0.322
3-methoxy-4-hydroxyphenylglycol 0.2487 0.0475 0.1276 0.2719
guanidinoacetate 0.2487 0.0475 0.3448 0.0023 ethyl glucuronide
0.2502 0.0461 0.1545 0.1826 3-hydroxypropanoate 0.2509 0.0455
0.1692 0.1439 N-acetylisoleucine 0.2511 0.0453 0.1146 0.3241
pregnen-diol disulfate 0.2515 0.045 0.1932 0.0944 thymol sulfate
0.2516 0.0449 0.2185 0.0579 citrate 0.252 0.0445 0.1569 0.1759
3-dehydrocholate 0.2537 0.0431 0.221 0.0551 sorbitol 0.2545 0.0424
0.1737 0.1334 argininosuccinate 0.2563 0.0409 0.1956 0.0905
glucosamine 0.2604 0.0377 0.1624 0.1611 N6-methyladenosine 0.2666
0.0332 0.1903 0.0996 S-methylcysteine 0.2688 0.0317 0.1516 0.1911
2-aminoadipate 0.2725 0.0294 0.2413 0.0357 5,6-dihydrouracil 0.2759
0.0273 0.2008 0.082 N-acetylaspartate (NAA) 0.2832 0.0234 0.1778
0.1245 xylitol 0.285 0.0225 0.1951 0.0913 N1-methyladenosine 0.2859
0.022 0.2608 0.0229 N6-acetyllysine 0.2981 0.0167 0.2376 0.0388
uracil 0.305 0.0142 0.3646 0.0012 4-androsten-3beta,17beta-diol
0.3071 0.0136 0.2664 0.02 disulfate 2 21-hydroxypregnenolone
disulfate 0.318 0.0104 0.219 0.0573 tryptophan 0.32 0.01 0.2654
0.0205 3-methyl-2-oxovalerate 0.3278 0.0082 0.2353 0.0408
N2-methylguanosine 0.3307 0.0076 0.3335 0.0032 ribitol 0.3366
0.0065 0.2194 0.0568 N-acetyl-beta-alanine 0.338 0.0063 0.2264
0.0493 ribulose 0.3382 0.0063 0.2708 0.018 glycolate
(hydroxyacetate) 0.3563 0.0039 0.3646 0.0012 gamma-aminobutyrate
(GABA) 0.3611 0.0034 0.2828 0.0133 thymine 0.3706 0.0026 0.3172
0.0052
[0119] In another example, using the patient serum samples
described in Example 1, samples with eGFR CKD-EPI values of 40-80
were further classified as having High or Low eGFR values. Patient
samples with eGFR values of 40-60 were classified as having Low
eGFR; patient samples with eGFR values of 61-80 were classified as
having High eGFR. A total of 41 patients were classified as having
Low eGFR, and 42 patients were classified as having High eGFR at
the time of sample collection.
[0120] The levels of metabolites were measured and the results were
analyzed using t-tests. Biomarkers for kidney function in patients
with intermediate eGFR measurements (e.g., CKD-EPI eGFR
calculations of 40-80) were analyzed by comparing High (eGFR
calculation of 61-80) vs. Low (eGFR calculation of 40-60) samples.
As listed in Table 4, the analysis resulted in the identification
of biomarkers that were differentially present between patient
serum samples with High eGFR and those with Low eGFR.
[0121] Table 4 includes, for each biomarker, the biochemical name
of the biomarker, the fold change of the biomarker in subjects with
High eGFR compared to subjects with Low eGFR (High/Low, is the
ratio of the mean level of the biomarker in samples from patients
with CKD-EPI eGFR of 61-80 compared to the mean level in samples
from patients with CKD-EPI eGFR of 40-60), and the p-value and
q-value determined in the statistical analysis of the data
concerning the biomarkers. Table 4 also lists the following: the
internal identifier for the biomarker compound (CompID); the
identifier for the biomarker compound in the Kyoto Encyclopedia of
Genes and Genomes (KEGG), if available; and the identifier for the
biomarker compound in the Human Metabolome Database (HMDB), if
available.
TABLE-US-00004 TABLE 4 Serum biomarkers to assess kidney function
in patients with eGFR of 40-80 HIGH/LOW Fold q- Comp Biochemical
Name Change p-value value ID KEGG HMDB pseudouridine 0.75 p <
0.0001 0.0009 33442 C02067 HMDB00767 N-acetylthreonine 0.79 p <
0.0001 0.0097 33939 C01118 C-glycosyltryptophan 0.74 p < 0.0001
0.0021 32675 N6- 0.73 p < 0.0001 0.0021 35157 HMDB41623
carbamoylthreonyladenosine N4-acetylcytidine 0.72 p < 0.0001
0.0097 35130 HMDB05923 erythronate 0.78 0.0001 0.0097 33477
HMDB00613 X-11564 0.76 0.0001 0.0097 32881 N1-methyladenosine 0.86
0.0002 0.0131 15650 C02494 HMDB03331 3-methylglutarylcarnitine (C6)
0.68 0.0004 0.02 37060 HMDB00552 5-methylthioadenosine (MTA) 0.62
0.0004 0.02 1419 C00170 HMDB01173 glycerophosphorylcholine 1.45
0.0007 0.0288 15990 C00670 HMDB00086 (GPC) ADpSGEGDFXAEGGGVR 2.54
0.0008 0.0288 33801 tryptophan 1.14 0.0009 0.0314 54 C00078
HMDB00929 N-formylmethionine 0.81 0.0013 0.0422 2829 C03145
HMDB01015 2-hydroxyisobutyrate 0.46 0.0015 0.0451 22030 HMDB00729
fucose 0.72 0.0017 0.0461 15821 C01018 HMDB00174 succinylcarnitine
0.75 0.0021 0.0553 37058 N-acetylserine 0.78 0.0027 0.0636 37076
HMDB02931 N-acetylalanine 0.88 0.0028 0.0636 1585 C02847 HMDB00766
4-acetamidobutanoate 0.81 0.0028 0.0636 1558 C02946 HMDB03681 1-
1.38 0.0032 0.0688 37231 docosapentaenoylglycerophosphocholine
(22:5n3) myo-inositol 0.75 0.0034 0.0722 19934 C00137 HMDB00211
gluconate 0.73 0.0046 0.0886 587 C00257 HMDB00625
1-linoleoylglycerol (1- 0.62 0.005 0.0907 27447 monolinolein)
ribitol 0.83 0.0058 0.0961 15772 C00474 HMDB00508
N1-Methyl-2-pyridone-5- 0.78 0.0061 0.0983 40469 C05842 HMDB04193
carboxamide arabitol 0.78 0.0071 0.1064 38075 C01904 HMDB01851
octadecanedioate 1.31 0.009 0.1233 36754 HMDB00782
eicosapentaenoate (EPA; 1.58 0.0093 0.1247 18467 C06428 HMDB01999
20:5n3) cortisol 0.86 0.0095 0.1247 1712 C00735 HMDB00063
erythritol 0.76 0.0119 0.1461 20699 C00503 HMDB02994 furosemide
0.47 0.0124 0.1461 43009 D00331 HMDB01933 caffeine 1.54 0.0126
0.1461 569 C07481 HMDB01847 1- 1.36 0.0127 0.1461 33822
docosahexaenoylglycerophosphocholine (22:6n3) ergothioneine 0.48
0.0127 0.1461 37459 C05570 HMDB03045 saccharin 3.34 0.0132 0.1481
21151 D01085 HMDB29723 guanosine 0.78 0.0137 0.1481 1573 C00387
HMDB00133 ethyl glucuronide 2.51 0.0141 0.1487 39603
N2,N2-dimethylguanosine 0.85 0.0155 0.1521 35137 HMDB04824
10-undecenoate (11:1n1) 1.37 0.0157 0.1521 32497 1-methylxanthine
1.45 0.0177 0.1618 34389 C16358 HMDB10738 theophylline 1.66 0.0181
0.1632 18394 C07130 HMDB01889 pregn steroid monosulfate 1.61 0.0187
0.1632 32619 N2,N5-diacetylornithine 0.71 0.0191 0.1632 43591
paraxanthine 1.43 0.0191 0.1632 18254 C13747 HMDB01860
pro-hydroxy-pro 0.75 0.0224 0.1747 35127 HMDB06695 8-aminocaprylate
2.17 0.0224 0.1747 21161 pantothenate 0.82 0.0227 0.1748 1508
C00864 HMDB00210 azelate (nonanedioate) 2.99 0.0232 0.1764 18362
C08261 HMDB00784 DSGEGDFXAEGGGVR 2.72 0.0239 0.1797 31548 1- 1.28
0.0261 0.1934 33228 C05208 arachidonoylglycerophosphocholine
(20:4n6) acisoga 0.78 0.0284 0.2034 43258 creatinine 0.89 0.0309
0.2144 513 C00791 HMDB00562 X-17299 0.87 0.0314 0.2144 40097 2-
1.32 0.0317 0.2144 35256 arachidonoylglycerophosphocholine
isoleucylleucine 1.28 0.032 0.2144 36760 ADSGEGDFXAEGGGVR 1.84
0.0341 0.2229 33084 1- 1.21 0.0342 0.2229 34419 C04100
linoleoylglycerophosphocholine (18:2n6) stearoyl sphingomyelin 1.15
0.0346 0.2229 19503 C00550 HMDB01348 indoleacetylglutamine 0.86
0.0366 0.2288 42087 HMDB13240 5-oxoproline 1.16 0.0371 0.2295 1494
C01879 HMDB00267 dimethylarginine (SDMA + 0.65 0.0377 0.2311 36808
C03626 HMDB01539 ADMA) ribose 0.71 0.0389 0.2314 12080 C00121
HMDB00283 urea 0.87 0.039 0.2314 1670 C00086 HMDB00294
docosahexaenoate (DHA; 1.21 0.0393 0.2314 19323 C06429 HMDB02183
22:6n3) threitol 0.7 0.0415 0.2401 35854 C16884 HMDB04136
propionylcarnitine 0.84 0.0443 0.2534 32452 C03017 HMDB00824
1,3-dihydroxyacetone 0.6 0.0458 0.2534 35963 C00184 HMDB01882
2-methylbutyrylcarnitine (C5) 0.77 0.0464 0.2547 35431 HMDB00378
2-aminobutyrate 1.19 0.0487 0.2624 32309 C02261 HMDB00650 xylonate
0.71 0.0497 0.2633 35638 C05411 HMDB60256
[0122] While the invention has been described in detail and with
reference to specific embodiments thereof, it will be apparent to
one skilled in the art that various changes and modifications can
be made without departing from the spirit and scope of the
invention.
* * * * *