US20210087629A1

US20210087629A1 - Methods for Treating and Detecting Sepsis in Humans

Info

Publication number: US20210087629A1
Application number: US17/038,496
Authority: US
Inventors: Christoph W. Sensen; Jung Soh; Petra Heidinger; Laura Villanova; Stefan Grabuschnig
Original assignee: Cna Diagnostics Inc
Current assignee: Cna Diagnostics Inc
Priority date: 2018-07-30
Filing date: 2020-09-30
Publication date: 2021-03-25
Also published as: US20200032336A1; WO2020026026A1; WO2020026026A4; US10793906B2

Abstract

Biomarkers for identifying sepsis in humans are presented herein, as are related methods, uses, agents, and kits comprising same. Methods for treating, detecting, and diagnosing sepsis in humans are presented herein.

Description

RELATED APPLICATIONS

This application is a continuation application of U.S. application Ser. No. 16/526,923, filed Jul. 30, 2019, which claims priority of and benefit to U.S. Provisional Application No. 62/711,970, filed Jul. 30, 2018, the entireties of each of which is incorporated herein by reference for all purposes.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jul. 25, 2019, is named 176395-010601_SL.txt and is 185,649 bytes in size.

FIELD OF INVENTION

Polynucleotides relating to circulating nucleic acids (CNAs) indicative of sepsis are described herein, as are probes, methods, and kits for detecting and diagnosing sepsis in humans. Also encompassed herein are probes, methods, and kits for detecting CNAs described herein in samples. In a particular embodiment, the CNAs are detected in samples isolated from humans.

BACKGROUND

Sepsis, also known as systemic inflammatory response syndrome, is a leading cause of mortality in mammals and is characterized by symptoms that include fever, elevated heart and breathing rate, and organ failure. Even under the best of care, sepsis can lead to septic shock which is frequently fatal. Sepsis is linked to immune responses to infection and more particularly to an excessive inflammatory immune response. Bacterial infections are the most common infection associated with sepsis, but fungal, viral, and parasitic infections can also lead to sepsis. Sepsis arises from a complicated interactive network of the causative agent (e.g., a bacterial infection) and the host immune system response to the agent. The genetic background of the host and the status of the host immune system contribute to the potential for developing sepsis and severity of the condition once developed. Early phases of sepsis are typically associated with high levels of inflammation due to the release of inflammatory cytokines, such as high mobility group box 1 protein (HMGB1) and tumor necrosis factor-alpha (TNF-α), interleukin-1 (IL-1), and interleukin-6 (IL-6). The dramatic release of such inflammatory cytokines, wherein a positive feedback loop is established between the cytokines and white blood cells, is referred to as a cytokine storm (also known hypercytokinemia or cytokine cascade). Later phases of sepsis are somewhat paradoxically associated with prolonged periods of reduced immune system activity.

SUMMARY

Methods, reagents, and kits described herein relate to predicting and/or diagnosing sepsis in a human in advance of the appearance of sepsis symptoms in the human. In accordance with the present experimental findings, methods, reagents, and kits described herein can be used to predict/diagnose sepsis in a human subject in advance of symptomatic presentation as well as in later stages of the disease progress. Indeed, results presented herein demonstrate that methods, reagents, and kits described herein can diagnose sepsis in a human subject at least three days in advance of clinical presentation. In light of results presented in the examples, over-representation or under-representation of at least one polynucleotide relative to an internal reference region in a biological sample or body fluid sample (e.g., serum), wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148, is a positive indicator that a human subject from which the sample was isolated is developing sepsis. Accordingly, the methods, reagents, and kits described herein provide for diagnosis of sepsis at early, pre-symptomatic stages of the disease, as well as later stages of the disease. Methods for determining over-representation or under-representation of at least one polynucleotide (CNA) relative to an internal reference region, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148, in body fluids are also disclosed, as are kits for such purposes, methods for screening the diagnostic target, and detection tests for screening. In a particular embodiment, the internal reference regions is at least one of SEQ ID NOs: 59, 61, or 68.
In a particular aspect, a method is presented comprising administering to a human identified as having sepsis a therapeutically effective amount of at least one agent used to treat sepsis, wherein the human is identified as having sepsis by analyzing a biological sample isolated from the human for over-representation or under-representation of at least one polynucleotide relative to an internal reference region, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148 and wherein the over-representation or under-representation of the at least one polynucleotide in the biological sample is indicative of sepsis, thereby identifying the human as having sepsis.
In another particular aspect, a method is presented comprising administering to a human identified as having over-representation or under-representation of at least one polynucleotide relative to an internal reference region a therapeutically effective amount of at least one agent used to treat sepsis, wherein the human is identified as having over-representation or under-representation of at least one polynucleotide relative to an internal reference region by analyzing a biological sample isolated from the human for over-representation or under-representation of at least one polynucleotide relative to an internal reference region, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148 and wherein the over-representation or under-representation of the at least one polynucleotide in the biological sample is a positive indicator that the human is in need of the administering.
In another particular aspect, a method is presented for detecting sepsis in a human, comprising
(a) analyzing a biological sample isolated from the human for over-representation or under-representation of at least one polynucleotide relative to an internal reference region, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148, by contacting the biological sample with at least one synthetic probe specific for a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148, wherein the contacting generates complexes of synthetic probes bound to specific polynucleotides when at least one polynucleotide comprising any one of 1-57 or 94-148 is present in the biological sample, (b) detecting the complexes of synthetic probes bound to specific polynucleotides, and detecting the internal reference region in the biological sample, and (c) comparing the at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 detected in the biological sample to the internal reference region detected in the biological sample to determine relative over-representation and under-representation of the at least one polynucleotide in the biological sample, wherein detection of the over-representation and under-representation of the at least one polynucleotide serves as a positive indicator of sepsis in the human.
In another particular aspect, a method is presented for detecting sepsis in a human, comprising analyzing a biological sample isolated from the human for over-representation or under-representation of at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 relative to an internal reference region, wherein detection of over-representation or under-representation of the at least one said polynucleotide relative to the internal reference region in the biological sample is a positive indicator of sepsis in the human.
In another particular aspect, a method is presented for detecting sepsis in a human, comprising detecting at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 in a biological sample obtained from the human wherein over-representation and under-representation of the at least one polynucleotide relative to an internal reference region in the biological sample is a positive indicator of sepsis in the human. The method may further comprising use of a therapeutically effective amount of at least one agent used to treat sepsis for treatment of the human.
In another particular aspect, a method is presented for evaluating representation of at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 in a biological sample of a human, the method comprising: analyzing the biological sample of the human for over-representation or under-representation of at least one polynucleotide relative to an internal reference region, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148, and wherein the over-representation or the under-representation of the at least one polynucleotide in the biological sample is determined by detecting the at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 in the biological sample, wherein the detecting is achieved by contacting the biological sample with at least one reagent that specifically binds to any one of SEQ ID NOs: 1-57 or 94-148, detecting the internal reference region in the biological sample, and comparing the at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 detected in the biological sample to the internal reference region detected in the biological sample to determine relative over-representation and under-representation of the at least one polynucleotide in the biological sample.
In a particular embodiment of any of the above methods, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148 over-represented or under-represented relative to the internal reference region, the at least one is at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, at least twenty, at least twenty-one, at least twenty-two, at least twenty-three, or at least twenty-four of the polynucleotides comprising any one of SEQ ID NOs: 1-57 or 94-148.
In a particular embodiment of any of the above methods, the biological sample is blood, a product derived from blood, or a fraction derived from blood. In a more particular embodiment, the product derived from blood is plasma or serum.
In a particular embodiment of any of the above methods, the internal reference region comprises at least one polynucleotide comprising any one of SEQ ID NOs: 59, 61, or 68.
In a particular embodiment of any of the above methods, detecting the over-representation or under-representation of the at least one polynucleotide relative to an internal reference region comprises at least one of a polymerase chain reaction (PCR)-based detection method, a hybridization-based method, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), solid-phase enzyme immunoassay (EIA), mass spectrometry, or microarray analysis. In a more particular embodiment, the PCR-based detection method is performed using at least one primer pair, wherein each primer pair of the at least one primer pair is specific for any one of SEQ ID NOs: 1-57 or 94-148, and a primer pair specific for at least one of SEQ ID NOs: 59, 61, or 68. In a more particular embodiment, the primer pair specific for any one of SEQ ID NOs: 1-57 or 94-148 and the primer pair specific for at least one of SEQ ID NOs: 59, 61, or 68 is any one of the primer pairs presented in Tables 1-3. In another particular embodiment, the method further comprises sequencing amplification products corresponding to any one of SEQ ID NOs: 1-57 or 94-148 or at least one of SEQ ID NOs: 59, 61, or 68 generated by the PCR-based detection method. In another particular embodiment, the SEQ ID NOs: (nucleic acid sequences) comprise circulating nucleic acid. In another particular embodiment, the at least one agent used to treat sepsis comprises at least one of an antibiotic, anti-fungal agent, anti-viral agent, anti-parasitic agent, or fluids suitable for intravenous administration. In another particular embodiment, the human is monitored for sepsis. In another particular embodiment, the over-representation or under-representation of the at least one polynucleotide relative to an internal reference region is determined using reagents comprising an antibody or a nucleic acid probe specific for any one of SEQ ID NOs: 1-57 or 94-148 and at least one of SEQ ID NOs: 59, 61, or 68. In another particular embodiment, the nucleic acid probe specific for any one of SEQ ID NOs: 1-57 or 94-148 and at least one of SEQ ID NOs: 59, 61, or 68 is labeled with a detectable label.
In another aspect, a probe comprising a manmade nucleotide sequence that binds specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 and at least one manmade tag conjugated thereto and at least one of SEQ ID NOs: 59, 61, or 68 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is complementary to the polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 and at least one of SEQ ID NOs: 59, 61, or 68. In a particular embodiment, the manmade nucleotide sequence that binds specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 and at least one of SEQ ID NOs: 59, 61, or 68 exhibits at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% complementarity to any one of SEQ ID NOs: 1-57 or 94-148 and at least one of SEQ ID NOs: 59, 61, or 68. In a particular embodiment, the manmade tag is a detectable marker. In a more particular embodiment, the detectable marker comprises a radioactive marker or fluorescent marker. In another embodiment, an array comprising at least one probe that binds specifically to any one of SEQ ID NOs: 1-57 or 94-148 and at least one of SEQ ID NOs: 59, 61, or 68 is presented, wherein the at least one probe is bound to a solid surface. In a particular embodiment, the array is used for diagnosing sepsis. In another embodiment, a kit comprising at least one probe that binds specifically to any one of SEQ ID NOs: 1-57 or 94-148 and at least one of SEQ ID NOs: 59, 61, or 68 is presented, wherein the kit further optionally comprises instructions for use thereof. In a particular embodiment, the kit is used for diagnosing sepsis. In another particular embodiment, the kit is used for detecting the indicated SEQ ID NOs:. In embodiments thereof, the array or kit comprises comprising at least four, five, or ten different probes comprising a manmade nucleotide sequence that binds specifically to a polynucleotide comprising any one of the SEQ ID NOs: listed in Table 4 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is complementary to the polynucleotide comprising any one of the SEQ ID NOs: listed in Table 4. In a particular embodiment, the array comprises a microarray, gene chip, DNA chip, or a FILMARRAY®.
In another aspect, a primer comprising, consisting essentially of, or consisting of a manmade nucleotide sequence that binds specifically to a polynucleotide comprising any one of the SEQ ID NOs: listed in Table 4 and at least one manmade tag conjugated thereto is presented, wherein the manmade nucleotide sequence is any one of the polynucleotide primer sequences or a primer pair listed in Tables 1-3 or a variant thereof. In a more particular embodiment, the variant of any one of the polynucleotide primer sequences listed in Tables 1-3 is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the polynucleotide sequences listed in Table 4. In another particular embodiment, the manmade tag is a detectable marker (e.g., a radioactive marker or fluorescent marker.
In another aspect, a kit for detecting sepsis in a human is presented comprising at least one primer pair for amplifying a polynucleotide comprising any one of the SEQ ID NOs: listed in Table 4, wherein the at least one primer pair is listed in Tables 1-3 and optionally, instructions for use thereof. In a particular embodiment, the at least one primer pair is four primer pairs and wherein each primer pair of the four primer pairs specifically amplifies a different polynucleotide comprising any one of the SEQ ID NOs: listed in Table 4. In another particular embodiment, the at least one primer pair is five primer pairs and wherein each primer pair of the five primer pairs specifically amplifies a different polynucleotide comprising any one of the SEQ ID NOs: listed in Table 4. In another particular embodiment, the at least one primer pair is ten primer pairs and wherein each primer pair of the ten primer pairs specifically amplifies a different polynucleotide comprising any one of the SEQ ID NOs: listed in Table 4.
In another aspect, use of a polynucleotide sequence comprising any one of the SEQ ID NOs: listed in Table 4 as a biomarker for the detection of sepsis in a human is encompassed herein. In a particular embodiment, the biomarker is a biomarker in a sample obtained from the human, wherein the sample is a sample of blood, a product derived from blood or a fraction derived from blood (e.g. plasma or serum)
In an aspect, a method for treating a human suspected of having sepsis is presented, the method comprising treating the human identified as having sepsis with a therapeutically effective amount of at least one agent used to treat sepsis, wherein the human is identifiable as having sepsis by analyzing a biological sample isolated from the human for over-representation or under-representation of at least one polynucleotide, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148 and wherein the over-representation or under-representation of the at least one polynucleotide in the biological sample is a positive indicator of sepsis. In a particular embodiment thereof, the over-representation or the under-representation of the at least one polynucleotide is determined relative to an internal reference region. In a particular embodiment, the internal reference regions is at least one of SEQ ID NOs: 59, 61, or 68.
Also encompassed herein is a therapeutically effective amount of at least one agent used to treat sepsis or a composition thereof for use in a method of treating sepsis in a human identified as having sepsis, wherein the human is identified as having sepsis by analyzing a biological sample isolated from the human for over-representation or under-representation of at least one polynucleotide, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148 and wherein the over-representation or under-representation of the at least one polynucleotide in the biological sample is a positive indicator of sepsis. The human may exhibit symptoms of sepsis or may be asymptomatic. In a particular embodiment thereof, the over-representation or the under-representation of the at least one polynucleotide is determined relative to an internal reference region. In a particular embodiment, the internal reference regions is at least one of SEQ ID NOs: 59, 61, or 68.
In another aspect, a method for treating a human identified as exhibiting over-representation or under-representation of at least one polynucleotide is presented, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148 and wherein the over-representation or the under-representation of the at least one polynucleotide in the biological sample is a positive indicator of sepsis, the method comprising treating the human identified as exhibiting the over-representation or the under-representation of the at least one polynucleotide with a therapeutically effective amount of at least one agent used to treat sepsis. In a particular embodiment thereof, the over-representation or the under-representation of the at least one polynucleotide is determined relative to an internal reference region. In another particular embodiment, the human is identifiable as having sepsis by analysis of a biological sample isolated from the human for the over-representation or the under-representation of the at least one polynucleotide, wherein the over-representation or the under-representation of the at least one polynucleotide may optionally be determined relative to an internal reference region. In a particular embodiment, the internal reference regions is at least one of SEQ ID NOs: 59, 61, or 68.
In yet another aspect, a method for treating a human with early stage sepsis (e.g., pre-symptomatic sepsis) is presented, the method comprising treating the human with early stage sepsis with a therapeutically effective amount of at least one agent used to treat sepsis, wherein the human is identifiable as having early stage sepsis by analyzing a biological sample isolated from the human for over-representation or under-representation of at least one polynucleotide, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148 and wherein the over-representation or under-representation of the at least one polynucleotide in the biological sample is a positive indicator of sepsis. In a particular embodiment thereof, the over-representation or the under-representation of the at least one polynucleotide is determined relative to an internal reference region. In a particular embodiment, the internal reference regions is at least one of SEQ ID NOs: 59, 61, or 68.
Also encompassed herein is a therapeutically effective amount of at least one agent used to treat sepsis or a composition thereof for use in a method of treating sepsis in a human identified with early stage sepsis, wherein the human is identified as having early stage sepsis by analyzing a biological sample isolated from the human for over-representation or under-representation of at least one polynucleotide, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148 and wherein the over-representation or under-representation of the at least one polynucleotide in the biological sample is a positive indicator of sepsis. The human may exhibit symptoms of sepsis or may be asymptomatic. In a particular embodiment thereof, the over-representation or the under-representation of the at least one polynucleotide is determined relative to an internal reference region.
Methods described herein comprise embodiments wherein the at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 over-represented or under-represented is at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, or at least twenty of the polynucleotides comprising SEQ ID NOs: 1-57 or 94-148. In a particular embodiment thereof, the over-representation or the under-representation of the at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, or at least twenty of the polynucleotides comprising SEQ ID NOs: 1-57 or 94-148 is determined relative to an internal reference region. In a particular embodiment, the internal reference regions is at least one of SEQ ID NOs: 59, 61, or 68.
In a further aspect, a method for evaluating representation of at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 in a biological sample of a human is presented, the method comprising:
analyzing the biological sample of the human for over-representation or under-representation of at least one polynucleotide, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148, and
wherein the over-representation or the under-representation of the at least one polynucleotide in the biological sample is determined by detecting the at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 in the biological sample, wherein the detecting is achieved by contacting the biological sample with at least one reagent that specifically binds to any one of SEQ ID NOs: 1-57 or 94-148, to determine relative over-representation and under-representation of the at least one polynucleotide in the biological sample. In a particular embodiment thereof, the over-representation or the under-representation of the at least one polynucleotide in the biological sample, when compared to an internal reference is determined; for example by quantitative real time polymerase chain reaction (RT-PCR). In accordance with methods described herein, amplification of regions of the CNAs represented by SEQ ID NOs: 1-57 or 94-148 involves a determination of how many amplification cycles are called for to reach a desired detection limit. In another particular embodiment, the over-representation or the under-representation of the at least one polynucleotide in the biological sample is determined by detecting the at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 in the biological sample, wherein the detecting is achieved by contacting the biological sample with at least one reagent that specifically binds to any one of SEQ ID NOs: 1-57 or 94-148, and detecting the internal reference region in the biological sample, and comparing the at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 detected in the biological sample to the internal reference region detected in the biological sample to determine relative over-representation and under-representation of the at least one polynucleotide in the biological sample. The over-representation or under-representation of the at least one polynucleotide may also be referred to herein as a deviation of the level of the at least one polynucleotide in the biological sample of an infected subject relative to the level of the at least one polynucleotide in a biological sample of a healthy subject.
Detection of the at least one polynucleotide may be achieved using RT-PCR as detailed herein as well as amplification free detection methods.
Methods described herein comprise embodiments wherein the biological sample is a bodily fluid, such as, without limitation, whole blood, a blood fraction, saliva, urine, sputum, cerebrospinal fluid, tears, sweat, milk, or interstitial fluid. In a particular embodiment, the biological sample is blood, a product derived from blood, or a fraction derived from blood. In a particular embodiment, the product derived from blood is plasma or serum.
Methods described herein comprise embodiments wherein detecting the over-representation or under-representation of the at least one polynucleotide comprises at least one of a PCR-based detection method (e.g., RT-PCR), a hybridization-based method, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (MA), solid-phase enzyme immunoassay (EIA), mass spectrometry, and microarray analysis. In a particular embodiment thereof, detecting the over-representation or under-representation of the at least one polynucleotide is determined relative to an internal reference region. In a particular embodiment, the internal reference regions is at least one of SEQ ID NOs: 59, 61, or 68.
In embodiments comprising a PCR-based detection method, the PCR-based detection method comprises amplifying nucleic acid sequences in the biological sample using primers that are specific for and capable of amplifying any one of SEQ ID NOs: 1-57 or 94-148, wherein the amplifying generates amplification products corresponding to any one of SEQ ID NOs: 1-57 or 94-148 when the biological sample comprises any one of SEQ ID NOs: 1-57 or 94-148. In embodiments comprising a PCR-based detection method, the PCR-based detection method is performed using at least one primer pair, wherein each primer pair of the at least one primer pair is specific for any one of SEQ ID NOs: 1-57 or 94-148. In a more particular embodiment thereof, the primer pair specific for any one of SEQ ID NOs: 1-57 or 94-148 is any one of the primer pairs presented in Table 1 or Table 3. In an even more particular embodiment thereof, the PCR-based detection method further comprises sequencing the amplification products corresponding to any one of SEQ ID NOs: 1-57 or 94-148. In a particular embodiment, the internal reference regions is at least one of SEQ ID NOs: 59, 61, or 68 and primer pairs therefor are presented in Table 2.
Methods described herein comprise embodiments wherein nucleic acid sequences comprise circulating nucleic acids.
Methods described herein comprise embodiments wherein the at least one agent used to treat sepsis comprises at least one of an antibiotic, anti-fungal agent, anti-viral agent, anti-parasitic agent, or fluids suitable for intravenous administration.
Methods described herein comprise embodiments wherein the human is monitored for sepsis.
Methods described herein comprise embodiments wherein the over-representation or under-representation of the at least one polynucleotide is determined using reagents comprising an antibody or a nucleic acid probe specific for any one of SEQ ID NOs: 1-57 or 94-148. In a particular embodiment thereof, the over-representation or under-representation of the at least one polynucleotide is determined relative to an internal reference region. In a more particular embodiment, the antibody is a monoclonal or a polyclonal antibody. In a still more particular embodiment, the antibody is obtained from mice, rats, rabbits, goats, chicken, donkey, horses or guinea pigs.
Methods described herein comprise embodiments wherein a nucleic acid probe specific for any one of SEQ ID NOs: 1-57 or 94-148 is labeled with a detectable label.
In another aspect, a probe comprising a manmade nucleotide sequence capable of binding specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 and at least one manmade tag conjugated thereto is presented, wherein the manmade nucleotide sequence is complementary to the polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148. In a particular embodiment thereof, the manmade nucleotide sequence capable of binding specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 exhibits at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% complementarity to any one of SEQ ID NOs: 1-57 or 94-148. In another particular embodiment, the manmade tag is a detectable marker. In a still more particular embodiment, the detectable marker comprises a radioactive marker or fluorescent marker.
Also encompassed herein is an array comprising at least one probe described herein, wherein the at least one probe is bound to a solid surface. Such arrays may comprise a microarray, gene chip, DNA chip, a FILMARRAY®, or a similar array.
Kits comprising at least one probe described herein and instructions for use thereof are also encompassed.
In a particular embodiment, the array or kit described herein comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, or at least twenty different probes comprising a manmade nucleotide sequence capable of binding specifically to corresponding polynucleotides comprising any one of SEQ ID NOs: 1-57 or 94-148 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is complementary to the polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148. In a particular embodiment, the array or kit described herein comprises at least four different probes comprising a manmade nucleotide sequence capable of binding specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is complementary to the polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148. In a more particular embodiment, the array or kit described herein comprises at least eight different probes comprising a manmade nucleotide sequence capable of binding specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is complementary to the polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148.
Also encompassed herein is a primer comprising a manmade nucleotide sequence capable of binding specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is any one of the polynucleotide sequences listed in Table 1 or Table 3 as a forward primer or a variant thereof or as a reverse primer or a variant thereof. In an embodiment thereof, the variant of any one of the primer sequences listed in Table 1 or Table 3 is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the primer sequences listed in Table 1 or Table 3. In a particular embodiment, a variant of a primer comprises different nucleotides at the 5′ end of the primer, which positions are more tolerant of variations thereto. In a particular embodiment, the manmade tag is a detectable marker (e.g., a radioactive marker, fluorescent dye), a tag that is specifically recognized (e.g., bound) by a labeled reagent (e.g., a labeled antibody), a tag that is specifically bound by a magnetic bead, or any other marker comprising detectable label.
Also encompassed herein are primers and probes for use in detecting the at least one polynucleotide described herein, wherein when using a TaqMan system, the detection of a particular polynucleotide sequence requires two specific primers (a forward and reverse primer pair specific for the polynucleotide sequence) and a probe (labeled oligonucleotide specific for the polynucleotide sequence). A labeled probe may, for example, be a TaqMan probe comprising a fluorescent label at a first terminus and a quencher at a second terminus whereby upon probe displacement during quantitative PCR (qPCR), the probe is cleaved, thus releasing the fluorescent label from the vicinity and effects of the quencher. Upon release from the vicinity/effects of the quencher, a higher fluorescence is emitted from the fluorescent label, which can be detected and quantitated to reflect the level/amount of the particular polynucleotide sequence present in a sample.
Also encompassed herein are methods for amplification-free detection of the at least one polynucleotide described herein, wherein such methods comprise a pair of oligonucleotide probes which are specific for the particular polynucleotide and are differentially labeled such that when each is bound to the polynucleotide and therefore in close proximity, the signal emitted from the probes changes. With respect to oligonucleotide probes that are labeled with fluorescent tags, close proximity of the fluorescent tags when bound to the polynucleotide is detected by an increase in fluorescence emissions.
Also encompassed herein is a primer consisting essentially of or consisting of a manmade nucleotide sequence capable of binding specifically to a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is any one of the polynucleotide sequences listed in Table 1 or Table 3 or a variant thereof. In an embodiment thereof, the variant of any one of the polynucleotide sequences listed in Table 1 or Table 3 is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the polynucleotide sequences listed in Table 1 or Table 3. In a particular embodiment, the manmade tag is a detectable marker (e.g., a radioactive marker or fluorescent marker).
Primer pairs complementary to SEQ ID NOs: 1-57 or 94-148 and suitable for PCR amplification are readily determined based on the sequences of SEQ ID NOs: 1-57 or 94-148 (5′ to 3′ strands) and reverse strands thereof (3′ to 5′ strands). Such primers are typically 8-20 nucleotides in length and are complementary (e.g., exhibit perfect complementarity or may be variants thereof that maintain a degree of complementarity sufficient to bind and act as primers in a PCR amplification) to any one of SEQ ID NOs: 1-57 or 94-148 or a reverse strand thereof. Choices regarding primer pairs suitable for PCR amplification are also determined based on the guanine/cytosine content of a potential primer sequence and the distance between the primers in a pair when bound to the target polynucleotide, with the understanding that PCR amplification products must be of a detectable size.
In another embodiment, therapeutic efficacy of a treatment regimen may be evaluated based on a change in the over-representation or under-representation of at least one of SEQ ID NOs: 1-57 or 94-148 following onset of the treatment regimen. In a particular embodiment, a decrease in representation of a CNA that is over-represented in sepsis (e.g., SEQ ID NOs: 94-148) is indicative that the treatment regimen is therapeutically effective. In another particular embodiment, an increase in representation of a CNA that is under-represented in sepsis (e.g., SEQ ID NOs: 1-57) is indicative that the treatment regimen is therapeutically effective.
Also encompassed herein is an array comprising at least one primer listed in Table 1 or Table 3, wherein the at least one primer is bound to a solid surface.
A kit for detecting sepsis in a human is also described, wherein the kit comprises at least one primer pair for amplifying a polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148, wherein the at least one primer pair is listed in Table 1 or Table 3 or a functional variant thereof or a primer that may be determined based on any one of the sequences designated herein as SEQ ID NOs: 1-57 or 94-148 and instructions for use thereof. In a particular embodiment, the at least one primer pair is four primer pairs and each primer pair of the four primer pairs specifically amplifies a different polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148. In another particular embodiment, the at least one primer pair is eight primer pairs and each primer pair of the eight primer pairs specifically amplifies a different polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148.
Additional aspects of the present invention will be apparent in view of the description which follows.
Additional aspects of the present invention will be apparent in view of the description which follows.

BRIEF DESCRIPTION OF THE FIGURES AND TABLES

The invention will now be described in relation to the drawings and tables.

FIGS. 1A-H presents Table 1, wherein each of the sequences corresponds to a CNA and is designated SEQ ID NO: 1-57 in consecutive order. SEQ ID NOs: 1-57 are positive indicators of sepsis that are more highly represented in healthy controls and thus, a decrease in copy number is observed during infection. Accordingly, a decrease in copy number of any one of SEQ ID NOs: 1-57 is a positive indicator of sepsis. Forward and reverse primers suitable for PCR amplification of each of SEQ ID NOs: 1-57 are presented in the same row as the CNA for which they are specific.

FIGS. 2A-F presents Table 2, wherein each of the Sequences corresponds to a CNA and is designated SEQ ID NO: 58-93 in consecutive order. SEQ ID NOs: 58-93 are equally represented in copy number in healthy controls and subjects afflicted with sepsis. Forward and reverse primers suitable for PCR amplification of each of SEQ ID NOs: 58-93 are presented in the same row as the CNA for which they are specific.

FIGS. 3A-I presents Table 3, wherein each of the Sequences corresponds to a CNA and is designated SEQ ID NO: 94-148 in consecutive order. SEQ ID NOs: 94-148 are positive indicators of sepsis that increase in copy number during infection. Forward and reverse primers suitable for PCR amplification of each of SEQ ID NOs: 94-148 are presented in the same row as the CNA for which they are specific.

DETAILED DESCRIPTION OF THE INVENTION

Various embodiments will be described in detail with reference to the drawings and tables. Reference to various embodiments does not limit the scope of the claims attached hereto. Additionally, any examples set forth in this specification are not intended to be limiting and merely set forth some of the many possible embodiments.
Methods, reagents, and kits described herein relate to detection and analysis of cell-free DNA available in the blood following active secretion, cell death or apoptosis. The present inventors have demonstrated that cell-free DNA indicative of sepsis can be detected in blood up to 2-3 days prior to clinical diagnosis of sepsis according to Sepsis-3-definition (defined below in accordance with current medical standards). Traditional biomarkers such as lactate, procalcitonin and others are measured only after clinical sepsis is evident from the patient's vital signs or labs. In high-risk patients, this may be too late to prevent the body's cascade of cytokine release, the harbinger of development for sepsis sequelae.
Accordingly, the lead-time provided by the present methods, reagents, and kits identifies subjects requiring heightened attention and monitoring. In particular embodiments, the present methods, reagents, and kits provide information on which basis a medical practitioner may initiate appropriate therapy and identify the site of infection, which may require source control, before the onset of irreversible organ dysfunction and widespread cellular hypoxia that occurs during the later stages of sepsis in septic patients.
Further to the above, methods described herein are based on the analysis of circulating nucleic acids, which are present in, for example, serum and plasma of humans. The composition and relative abundance of circulating nucleic acids varies depending on disease state. The present inventors identified particular genomic regions that do not change in relative abundance of specific regions of circulating nucleic acids between sepsis patients and controls (non-sepsis), which genomic regions are designated internal reference regions. Genomic regions that significantly vary in abundance between sepsis patients and controls were also identified and designated disease motifs. Relative abundance for disease motifs can be examined using Real-Time Polymerase Chain Reaction (RT-PCR) to determine if an “unknown” sample can be identified as exhibiting features characteristic of sepsis or features characteristic of non-sepsis. In a particular embodiment, identifying a sample as exhibiting features characteristic of sepsis may be used to predict onset of sepsis or diagnose sepsis.
It is to be understood that combinations of primers binding to genomic regions that significantly vary in coverage and abundance between sepsis patients can be optimized. The RT-PCR assay can be designed based at least in part on primers used and such an assay can be used to identify early features of sepsis.
Probes, methods, and kits described herein can analyze cell free DNA (cfDNA) collected at a preclinical stage of sepsis and accurately determine which patients will go on to develop sepsis. This preclinical phase includes patients that already have molecular evidence of an infection but have not yet manifested traditional criteria including vital sign abnormalities, fever and laboratory changes (according to the Sepsis-3-definition).
Early identification of sepsis, formerly known as septicaemia, is clinically valuable because sepsis has a high morbidity and mortality rate in mammals in general and, even under the best of care, in humans. Sepsis is characterized as a systemic, excessive inflammatory response, which is frequently triggered by infection and proceeds unchecked by normal regulatory controls. Sepsis is most often associated with bacterial infections in humans. Severe trauma can also lead to systemic responses that adversely affect adaptive and innate immune responses, leading to excessive inflammation having pathological consequences. Severe trauma patients, such as burn and accident victims, may subsequently be afflicted with infections, some of which lead to sepsis. Clinical symptoms of sepsis in humans include lethargy, fever/hyperthermia in early stages of sepsis, confusion, and/or hypothermia in end-stage sepsis (e.g., septic shock).
Sepsis is a leading cause of hospitalization in the United States and is one of the most expensive conditions to treat because it typically requires a stay in the Intensive Care Unit (ICU) to achieve patient recovery. It has been estimated that 19 million patients will develop sepsis worldwide each year and this estimate likely substantially underestimates the problem. Indeed, sepsis is a leading cause of death, morbidity, and medical expense. Sepsis contributes to one-third of deaths of hospitalized patients. The mortality rate is estimated to be between 20% and 80%, depending on the cause of the sepsis and progression of sepsis. Onset of sepsis in patients following a hospital stay is frequent and particularly challenging, at least in part, because such patients are likely still in a state of recovery and therefore, physiologically weakened. Such patients may be in early, pre-clinical stages of sepsis upon release, but absent the present discoveries, sepsis cannot be detected at pre-clinical stages of the disease. Re-admittance to hospitals is a significant problem as it is costly and typically not covered in full by medical insurance policies. Indeed, people with sepsis are two to three times more likely to be readmitted to the hospital as people released from the hospital who were diagnosed with a variety of conditions, including heart failure, pneumonia, and chronic obstructive pulmonary disease. It is also noteworthy that a bout of sepsis can have lifelong ramifications for patients who are successfully treated and survive. As the number of sepsis survivors grows, it has become increasingly apparent that sepsis frequently leads to long-lasting physical and cognitive impairment.
Indeed, the growing number of patients who survive the acute phase of sepsis has revealed that the danger associated with the disease extends long after discharge from the hospital. Long-term mortality following a bout of sepsis is approximately 50% in the first year and rises to >81% over five years post-discharge. Sepsis survivors are also more prone to exhibit diminished physical and/or cognitive function following the bout of sepsis than age-matched controls hospitalized for unrelated indications. As a consequence of these diminished functions, many sepsis survivors are unable to return to the workforce.
The standard of care for treatment of bacterial sepsis in humans calls for aggressive use of antimicrobial therapy (e.g., antibiotics, anti-fungal agent, anti-viral agent), anti-parasitic agent therapy, and/or intravenous fluid therapy, which may be administered in conjunction with anti-inflammatory therapy. The choice of antibiotic used for treating a septic patient depends on the type of bacteria that infected the subject, which infection subsequently led to sepsis in the subject. Methods for culturing and identifying bacteria in samples isolated from a subject are known in the art. Broad-spectrum antibiotics are recommended within one hour after sepsis recognition/diagnosis. Beta-lactam antibiotics having broad coverage administered in combination with fluoroquinolones, macrolides, or aminoglycosides are recommended for severe cases of sepsis. An exemplary inflammatory therapy involves administration of non-steroidal anti-inflammatory agents to a human afflicted with bacterial sepsis.
Fungal infections are treated with anti-fungal medications specific to the particular fungus that caused the infection. These may be used in a cream or ointment, suppository, or pill form. Candida species are the predominant agent of fungal sepsis and account for about 5% of all cases of severe sepsis and septic shock in the United States. The antifungal armamentarium has expanded considerably with the advent of lipid formulations of amphotericin B, the newest triazoles and the echinocandins. Clinical trials have shown that the triazoles and echinocandins are efficacious and well tolerated antifungal therapies.
Prospective treatments for specific viruses implicated in sepsis are being developed. Pleconaril is an antiviral against enteroviral infection which inhibits viral attachment to the hosts cell receptors and prevents uncoating of the viral nucleic acids. Examples of ativiral agents that may be beneficial in presentations of sepsis in certain situations include acyclovir, which has been proven effective in HSV infections, amantadine, rimantadine, oseltamivir, and zanamivir for influenza, and more broad-spectrum antiviral drugs like ribavirin and favipiravir.
Parasite infections can lead to sepsis. For Giardia infections, a medication like metronidazole (Flagyl), tinidazole (Tindamax) or nitazoxanide (Alinia) may be used. For Chagas disease, antiparasitic medications such as benznidazole and nifurtimox may be used. For tapeworm, the most commonly used medications are praziquantel (Biltricide), aibendazole (Albenza), and nitazoxanide (Alinia). However, if the infection has progressed and become more invasive, you may need treatment with anti-inflammatory medications, anti-seizure medications, a shunt to drain fluid from your brain, or surgery to remove cysts caused by the tapeworm. For roundworm, the most commonly used medications include medendazole (Vermox), albdendazole (Albenza) and ivermectin (Stromectol). Surgery could be required to remove the worm if there is a bowel obstruction.
The following guidelines provide the standard of care for sepsis patients as established by the American Medical Association:
Managing Infection:
Antibiotics: Administer broad-spectrum intravenous antimicrobials for all likely pathogens within 1 hour after sepsis recognition (strong recommendation; moderate quality of evidence [QOE]).
Source control: Obtain anatomic source control as rapidly as is practical (best practice statement [BPS]).
Antibiotic stewardship: Assess patients daily for de-escalation of antimicrobials; narrow therapy based on cultures and/or clinical improvement (BPS).
Managing Resuscitation:
Fluids: For patients with sepsis-induced hypoperfusion, provide 30 mL/kg of intravenous crystalloid within 3 hours (strong recommendation; low QOE) with additional fluid based on frequent reassessment (BPS), preferentially using dynamic variables to assess fluid responsiveness (weak recommendation; low QOE).
Resuscitation targets: For patients with septic shock requiring vasopressors, target a mean arterial pressure (MAP) of 65 mm Hg (strong recommendation; moderate QOE).
Vasopressors: Use norepinephrine as a first-choice vasopressor (strong recommendation; moderate QOE).
Mechanical Ventilation in Patients with Sepsis-Related Acute Respiratory Distress Syndrome (ARDS):
Target a tidal volume of 6 mL/kg of predicted body weight (strong recommendation; high QOE) and a plateau pressure of ≤30 cm H₂O (strong recommendation; moderate QOE). See, for example, Howell and Davis (2017, JAMA 317:847).
As indicated hereinabove, sepsis is associated with multiple organ failure and high mortality. Commonly used markers for diagnosis of sepsis include: elevated leukocyte counts and elevated cytokine levels such as IL-6, IL-8 and IL-18, C-reactive protein, and procalcitonin. The latter two proteins are expressed at higher levels after trauma. With respect to procalcitonin, determination of procalcitonin levels is viewed as a helpful diagnostic marker, but is not viewed as a definitive marker of sepsis. Soluble urokinase-type plasminogen activator receptor (SuPAR) is considered to be a nonspecific marker of inflammation, but has prognostic value in the context of sepsis because higher SuPAR levels are associated with higher mortality in sepsis patients.
None of these markers provides a predictive indicator of sepsis, but rather collectively serve as indicators only upon onset of sepsis. Indeed, in advance of the present findings, a reliable method to predict risk for or diagnose sepsis in advance of the onset of clinical symptoms did not exist. As detailed herein, the methods, reagents, and kits described herein make it possible to diagnose patients with sepsis at pre-clinical stages and thus, make it possible to treat such patients in advance of the onset of clinical symptoms and at the least reduce the severity of acute sepsis in the patient should the patient progress toward disease despite early intervention.
Exemplary Target Patient Populations
Adult patients admitted to, for example, a hospital who are at high-risk for developing sepsis include the following:

- Victims of trauma with either an Injury Severity Score of ≥15 or a Glasgow Coma Score of ≤8 on hospital presentation;
- Any patient undergoing high-risk surgical procedures including any emergency surgery, high risk elective surgery procedures involving the thorax, esophagus, stomach, small bowel, large bowel; or
- Any patient being admitted to any intensive care unit (ICU) setting for any reason with no current evidence or suspicion of active infection as determined by primary team of attending medical practitioners.

Methods, reagents, and kits described herein relate to predicting and/or diagnosing sepsis in a human in advance of the appearance of symptoms of sepsis in the human. In accordance with the experimental findings presented herein, methods, reagents, and kits described are useful for diagnosing sepsis in a human subject in advance of symptomatic presentation. Indeed, results presented herein demonstrate that methods, reagents, and kits described herein can diagnose sepsis in a human subject at least three days in advance of clinical presentation. In light of results presented in the Examples, detection of over-representation or under-representation of at least one polynucleotide relative to an internal reference region in a body fluid sample (e.g., serum) isolated from a human subject, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148, is a positive indicator that the human subject will develop sepsis symptoms. Accordingly, the methods, reagents, and kits described herein provide for diagnosis of sepsis at pre-clinical stages of the disease. Also encompassed herein are methods to assess over-representation or under-representation of at least one polynucleotide relative to an internal reference region, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148, in body fluids and kits for such purposes.
In addition to plasma or serum, over-representation or under-representation of at least one polynucleotide (at least one of SEQ ID NOs: 1-57 or 94-148) relative to an internal reference region may be determined in other body fluids isolated from a human subject including: whole blood, a product derived from blood, or any fraction derived from blood (in addition to plasma or serum.
Any known method may be used for the determination of over-representation or under-representation of at least one polynucleotide (at least one of SEQ ID NOs: 1-57 or 94-148) relative to an internal reference region in body fluids. Methods encompassed for such determinations include: polymerase chain reaction (PCR) amplification with sequence specific primer pairs, a hybridization-based method, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), solid-phase enzyme immunoassay (EIA), mass spectrometry, microarray analysis, and any combination thereof. Such methods when used for determining risk for developing sepsis or predicting onset of sepsis are encompassed herein.
In a particular method for determining over-representation or under-representation of any one of SEQ ID NOs: 1-57 or 94-148 relative to an internal reference region in human body fluids, e.g. serum, the method calls for PCR amplification with sequence specific primer pairs. In an embodiment thereof, the PCR amplification is performed with at least one primer pair specific for any one of SEQ ID NOs: 1-57 or 94-148. Exemplary primer pairs for amplifying any one of SEQ ID NOs: 1-57 or 94-148 are presented in Table 1 or Table 3. Conditions for performing PCR amplifications are known in the art and presented in the Examples herein below. Such conditions may be determined based in part on the composition of a primer and/or primer pair and considerations relating to same are known in the art.
In another particular method for determining over-representation or under-representation of any one of SEQ ID NOs: 1-57 or 94-148 relative to an internal reference region in human body fluids, e.g. serum, the method calls for an ELISA. In one embodiment, the ELISA for at least one of SEQ ID NOs: 1-57 or 94-148 involves a sandwich array. In such an embodiment, PCR amplification of at least one of SEQ ID NOs: 1-57 or 94-148 may be performed as an initial step. Conventional microtiter plates may be coated with a first antibody, e.g. a guinea pig polyclonal antibody, directed against any one of SEQ ID NOs: 1-57 or 94-148. The plates are then blocked and the sample or reference is loaded. After incubation with, e.g., at least one of SEQ ID NOs: 1-57 or 94-148, a second antibody against any one of SEQ ID NOs: 1-57 or 94-148 is applied, e.g. a polyclonal rabbit antibody. A third antibody that detects the second antibody, e.g. an anti-rabbit antibody, conjugated to a suitable label, e.g. an enzyme for chromogenic detection, is then added. The plate is then developed with a substrate for the label in order to detect and quantify the label, which in turn serves as a measure of any one of SEQ ID NOs: 1-57 or 94-148 in the body fluid. This determination may then be compared to that of an internal reference region measured by similar methodology. If the label is an enzyme for chromogenic detection, the substrate is a color-generating substrate of the conjugated enzyme and the color reaction is subsequently detected in a microplate reader and compared to standards.
Suitable pairs of antibodies that may be used as first and second antibodies are any combination of, e.g., guinea pig, rat, mouse, rabbit, goat, chicken, donkey or horse antibodies. In a particular embodiment, the antibodies are polyclonal antibodies. In another particular embodiment, the antibodies are monoclonal antibodies or antibody fragments. Suitable labels include: chromogenic labels (enzymes that can be used to convert a substrate to a detectable colored or fluorescent compound), spectroscopic labels (e.g., fluorescent labels), and affinity labels which may be developed by an additional compound specific for the label, thereby facilitating detection and quantification, or any other label used in standard ELISA.
Other preferred methods for detection of any one of SEQ ID NOs: 1-57 or 94-148 include radioimmunoassay or competitive immunoassay using a single antibody and chemiluminescence detection on automated commercial analytical robots. Microparticle enhanced fluorescence, fluorescence polarized methodologies, or mass spectrometry may also be used. Detection devices, e.g. microarrays, are also useful components as readout systems for any one of SEQ ID NOs: 1-57 or 94-148.
Also encompassed herein are kits for assessing over-representation or under-representation of any one of SEQ ID NOs: 1-57 or 94-148 relative to an internal reference region for determining risk for developing sepsis, which kits may comprise apparatus and reagents for detecting at least one of SEQ ID NOs: 1-57 or 94-148. Apparatus and reagents considered for PCR amplification include: suitable PCR primer pairs specific for each of SEQ ID NOs: 1-57 or 94-148, amplification reagents, and thermocycling devices. With respect to ELISA, microtiter plates for ELISA, pre-coated ELISA plates, and plate covers are encompassed. Reagents useful for ELISA include those antibodies and solutions developed and designed for detecting each of SEQ ID NOs: 1-57 or 94-148. Standard solutions comprising each of SEQ ID NOs: 1-57 or 94-148 as positive controls may be included in such kits. Kits may further comprise hardware, such as pipettes, solutions such as buffers, blocking solutions and the like, filters, and directions for use thereof.
The following definitions are presented as an aid to understand the invention.
The term “DNA” means a polymer composed of deoxyribonucleotides.
The terms “sample”, “biological sample”, “diagnostic sample”, and the like refer to a material known or suspected of containing one or more polynucleotide or polypeptide markers. The diagnostic sample may be any tissue ((e.g., blood, and fractions thereof, including serum, etc.).
The terms “polynucleotide” and “nucleic acid”, used interchangeably herein, describe a polymer of any length, e.g., greater than about 10 bases, greater than about 100 bases, greater than about 500 bases, greater than 1000 bases, usually up to about 10,000 or more bases composed of nucleotides, such as deoxyribonucleotides or ribonucleotides, or compounds produced synthetically which can hybridize with naturally occurring nucleic acids in a sequence specific manner analogous to that of two naturally occurring nucleic acids in Watson-Crick base pairing interactions. Polynucleotide and nucleic acid include polynucleotides that encode a native-sequence polypeptide, a polypeptide variant, a portion of a polypeptide, a chimeric polypeptide, or an isoform, precursor, complex, modified form, or derivative of any of the foregoing, and any precursors thereof. Polynucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase or by a synthetic reaction. A polynucleotide may be modified after synthesis (e.g., by conjugation with a label, such as a radioactive, chemiluminescent, chemiflourescent, or fluorescent label, and the like). Other types of modifications to polynucleotides known to a person skilled in the art include substitution of one or more naturally-occurring nucleotides with an analog, internucleotide modifications (e.g., uncharged linkages, charged linkages), and the like.
Polynucleotides can also include circulating nucleic acids (“CNA”). The term “circulating nucleic acid” or “CNA” refers to free nucleic acid, including RNA and DNA, circulating in any form in the blood. CNA can include gene transcripts, transcription factors or other polynucleotide sequences. CNA can be obtained from any applicable biological sample, including blood, plasma, serum, and the like.
“Variants” of the sequences described herein are sequences wherein at least one nucleotide differs from that of the native or wild-type sequence (or the complement thereof), by virtue of an insertion, deletion, modification and/or substitution of one or more nucleotides within the native sequence. Such variants generally have less than 100% sequence identity relative to a native sequence or its complement. Accordingly, a sequence variant may have a nucleotide sequence with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity relative to the native or wild-type sequence or complement thereof. Variants, furthermore, may include fragments of any length that retain a biological activity of the corresponding native sequence. Variants also include sequences wherein one or more nucleotides are added to the 5′ or 3′ end of, or within, a native sequence or its complement.
“Percent sequence identity” is defined herein as the percentage of nucleotides or amino acid residues in the candidate sequence that are identical to the nucleotides or residues in the sequence of interest after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Methods and computer programs for the alignment of sequences are well known in the art, including, for example, “BLAST” algorithms.
“Oligonucleotides” include short, single-stranded polynucleotides that are at least seven nucleotides in length and less than about 250 nucleotides in length. The term “polynucleotides” includes oligonucleotides.
“Label” refers to a detectable compound or composition and “labelling” refers to the conjugation, fusion, or attachment of a detectable compound or composition to another. In some aspects described herein, the label is conjugated or fused directly or indirectly to a reagent, such as a polynucleotide probe or an antibody, and assists with the detection of the reagent to which it is conjugated or fused. The label itself can also be detectable (such as radioisotope labels or fluorescent labels and the like). In some aspects described herein, the label is an enzymatic label which catalyzes chemical alteration of a substrate compound or composition and results in a detectable product.
The term “diagnosis”, as used herein, refers to the identification or classification of a molecular or pathological state, disease, or condition (e.g., sepsis). In a particular embodiment, sepsis is diagnosed in a subject (e.g., a human subject) in advance of onset of sepsis symptoms.
In a particular embodiment, a human subject is characterized as being “at risk for developing sepsis” because they have recently experienced an accident (e.g., vehicular, bicycle), physical trauma (e.g., due to burns resulting from exposure to, e.g., fire or chemicals; knife or gunshot wounds; blunt force trauma; explosion), surgery, and/or infection (e.g., a bacterial, fungal, or viral infection). Human subjects at risk for developing sepsis also include: subjects with weakened immune systems (e.g., immunocompromised subjects); subjects with pre-existing infections or medical conditions (e.g., type 2 diabetes, kidney disease, and asthma), obese subjects, and very young and very old subjects, and subjects injured in contaminated environments. Assays to evaluate risk for developing sepsis may also be implemented on all patients admitted to the hospital and/or released from the hospital as a matter of routine.
In a particular embodiment thereof, each patient released after a hospital stay comprising at least one overnight stay is assayed using methods described herein to evaluate whether the patient has early stage sepsis or is at risk for developing sepsis post-release. In that the expense involved in re-admittance to the hospital is substantial and insurance coverage is not commensurate with such expenses, screening all patients released after at least one overnight stay, would be a cost-effective way in which to provide better healthcare to the patient and minimize expenditures involved with same.
Further to the above, exemplary indications for use include:

- At hospital admission where the best option today is to observe symptoms and run a series of blood cultures which normally takes over 24 hours for results and have high error rates;
- On high risk patient groups in hospitals where early identification and treatment of sepsis could have an impact to a patient's survival;
- On discharge where ruling out sepsis could lead to early discharge;
- In long term care facilities where the frequency of sepsis is high and early diagnosis and appropriate monitoring and/or treatment thereafter could potentially reduce costly re-admissions and/or admissions to hospitals; and
- Monitoring neonates for neonatal sepsis

Sepsis-3 Definitions

Sepsis is life-threatening organ dysfunction due to a dysregulated host response to infection
Sepsis clinical criteria: organ dysfunction is defined as an increase of 2 points or more in the Sequential Organ Failure Assessment (SOFA) score

- for patients with infections, an increase of 2 SOFA points gives an overall mortality rate of 10%
- Patients with suspected infection who are likely to have a prolonged ICU stay or to die in the hospital can be promptly identified at the bedside with qSOFA (“HAT”); i.e. 2 or more of:
  - Hypotension: SBP less than or equal to 100 mmHg
  - Altered mental status (any GCS less than 15)
  - Tachypnoea: RR greater than or equal to 22.

Septic shock is a subset of sepsis in which underlying circulatory and cellular/metabolic abnormalities are profound enough to substantially increase mortality

- Septic shock clinical criteria: Sepsis and (despite adequate volume resuscitation) both of:
  - Persistent hypotension requiring vasopressors to maintain MAP greater than or equal to 65 mm Hg, and
  - Lactate greater than or equal to 2 mmol/l,
- With these criteria, hospital mortality is in excess of 40%.

“Primer” refers to a polynucleotide capable of acting as a point of initiation of synthesis along a complementary strand when conditions are suitable for synthesis of a primer extension product. The synthesizing conditions include the presence of four different nucleotide bases (adenosine, cytidine, guanosine, thymidine/uridine) and at least one polymerization-inducing agent such as a reverse transcriptase or a DNA polymerase. The primers are present in a suitable buffer, which may include constituents which are co-factors or affect conditions such as pH and the like at various suitable temperatures. Primer includes single-stranded polynucleotide that is capable of hybridizing to nucleic acid and allowing the polymerization of a complementary nucleic acid, generally by providing a free 3′-OH group. Double stranded sequences can also be utilized. Primers are typically at least about 15 nucleotides. In some embodiments, primers can have a length of from about 15 to about 30, about 15 to about 50, about 15 to about 75, about 15 to about 100, or about 15 to about 500 nucleotides.
Exemplary primer pairs specific for each of SEQ ID NOs: 1-57 or 94-148 are presented herein in Table 1 or Table 3. Exemplary primer pairs specific for each of SEQ ID NOs: 58-93 are presented herein in Table 2. Such primer pairs are selected based on their specificity for a particular polynucleotide and may be optimized for use in connection with, e.g., PCR amplification. Polynucleotide-specific primer pairs may comprise primers that include variations within their sequence such that the primer is no longer 100% complementary to the polynucleotide for which it is specific. Primers comprising such variations are encompassed herein as long as the variations do not alter the ability of the primer to amplify the polynucleotide with specificity. Such variations may also include nucleotides and/or tags at the 5′ and 3′ ends of the primer that are not complementary the polynucleotide for which the primer is specific. It is also understood that a primer or primer pair may be complementary to sequences that flank any one of SEQ ID NOs: 1-148 in the human genome and thus, may be used to amplify one of SEQ ID NOs: 1-148 in keeping with methods described herein. Design of such primers and primer pairs is well within the capabilities of one of ordinary skill in the art having read the present specification.
In a particular embodiment, multiplex PCR based on the TaqMan approach is utilized to detect CNAs of interest. Such embodiments call for a primer pair, wherein each of the primers is specific for the particular CNA (polynucleotide) of interest and one labeled probe which is specific for the particular CNA (polynucleotide) of interest and labeled at each terminus with a different moiety. In a particular embodiment, the different moiety can be a fluorophore at the first terminus and a quencher at the second terminus. Such fluorophore-quencher pairs comprise, for example, FAM-BHQ1, HEX-BHQ1, LC610-BHQ2, CY5-BHQ-2, and CY5.5-BBQ650. Other pairs useful for this embodiment are known in the art.
A “motif” or “sequence motif” refers to a nucleotide sequence pattern that is generally conserved across multiple species. Polynucleotides can be derived from the motif. The polynucleotides can correspond to the entire sequence of the motif or a portion or portions of the motif.
“Marker” or “biomarker” refers to an indicator which can be detected in a sample, and includes predictive, diagnostic, and prognostic indicators and the like. The marker can be an indicator of a particular disease or disorder (e.g., sepsis) having certain molecular, pathological, histological, and/or clinical features. Exemplary biomarkers include, without limitation, polynucleotides, polypeptides, polypeptide and polynucleotide modifications (such as post-translational modifications and the like), carbohydrates, and/or glycolipid-based molecular markers. The “presence”, “amount”, or “level” of a marker associated with an increased clinical benefit to an individual is a detectable level of the marker in a sample. The presence, amount, or level of a marker can be measured by methods known to a person skilled in the art. The presence, amount, or level of a marker may be measured prior to treatment, during treatment, after treatment, or a combination of any of the foregoing.
“Internal reference region” refers to a nucleic acid fragment circulating in a bodily fluid (e.g., blood or a fraction thereof such as serum) that is present in the same amount in both control subjects (those subjects who do not have sepsis, those subjects who are not at risk for developing sepsis, and/or those subjects who do not develop sepsis in three days) and subjects who have sepsis, as determined, for example, by RT-PCR experiments. Internal reference regions provide a nucleic acid fragment which is represented in the bodily fluid at a particular level, against which representation of other nucleic acid sequences (e.g., any one of SEQ ID NOs: 1-57 or 94-148), which differ in control subjects and sepsis patients and are therefore discriminatory, can be evaluated in a relative manner. An internal reference system can be at least one region but can also be a composition of a few regions.
“Over-representation” refers to a fold increase (relative quantity RQ) relative to the internal reference region calculated as at least 2^{−delta-delta Cq}of 2.
“Under-representation” refers to a fold decrease (relative quantity RQ) relative to the internal reference region calculated as at most 2^{−delta-delta Cq}of 0.5.
The ΔCq method normalizes disease-specific motifs within a sample by subtracting the Cq value of the internal reference region (reference motif) from the Cq value of the disease specific motifs.
The 2−ΔΔCq method calculates relative quantity (RQ) of normalized disease specific motifs between two sample types (i.e., healthy and diseased). Information from multiple reference motifs can be combined to improve accuracy.
In a PCR reaction, the Cq (Cycle Quantification) value is the PCR cycle number at which the sample's reaction curve intersects the threshold line. This value tells how many cycles it took for the PCR machine to detect a real signal from the sample. Therefore, lower Cq values indicate higher amounts of target nucleic acid fragments, whereas higher Cq values indicate lower amounts of target nucleic acid fragments.
Exemplary CNAs identified herein, which are markers of sepsis, include SEQ ID NOs: 1-57 and 94-148. See Tables 1 and 3 (FIGS. 1 and 3). Exemplary primer pairs for amplifying each of SEQ ID NOs: 1-57 and 94-148 are also presented in Tables 1 and 3 (FIGS. 1 and 3). Reference is made to the chromosomal locations to which each of these CNAs can be found in the human genome. Accordingly, longer polynucleotides comprising each of SEQ ID NOs: 1-57 and 94-148, respectively, can readily be determined via access to publicly available databases. Additional primers for amplifying each of SEQ ID NOs: 1-57 and 94-148, respectively, can be designed based on the availability of such additional sequence information.
Exemplary subsets of SEQ ID NOs: 1-57 and 94-148 comprise at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, at least twenty, at least twenty-one, at least twenty-two, at least twenty-three, or at least twenty-four of the polynucleotides. Exemplary subsets and primers for amplification of each of the markers offer reagents for detecting CNAs comprising the indicated SEQ ID NOs:. See Tables 1-3. In a particular embodiment, detecting CNAs comprising the indicated SEQ ID NOs: is indicative of sepsis.
An exemplary subset may be provided in a kit for detecting at least one of SEQ ID NOs: 1-148 and subsets thereof (see, e.g., Table 4).
Table 4 presents an exemplary subset comprising, consisting essentially of, and/or consisting of the indicated SEQ ID NOs: 1-2, 4-6, 30-31, 38, 44, 46, 50, 53, 55, 59, 61, 68, 100, 108-110, 112, 114, 116, and 129. Primers for amplification of each of the markers listed in Table 4 can be found in the corresponding Tables 1, 2, or 3. Also encompassed herein are kits comprising the 24 exemplary markers presented in Table 4 and subsets thereof.

TABLE 4

List of 24 Exemplary Markers

Listed in	Final motif ID	SEQ ID NO:	Patent ID

Table 1	Sepsis JC1	1	hu-sep-CNAD-0001
Table 1	Sepsis JC2	2	hu-sep-CNAD-0002
Table 1	Sepsis JC4	4	hu-sep-CNAD-0004
Table 1	Sepsis JC5	5	hu-sep-CNAD-0005
Table 1	Sepsis JC6	6	hu-sep-CNAD-0006
Table 1	Sepsis JC34	30	hu-sep-CNAD-0030
Table 1	Sepsis JC35	31	hu-sep-CNAD-0031
Table 1	Sepsis JC42	38	hu-sep-CNAD-0038
Table 1	Sepsis JC48	44	hu-sep-CNAD-0044
Table 1	Sepsis JC50	46	hu-sep-CNAD-0046
Table 1	Sepsis SC2	50	hu-sep-CNAD-0050
Table 1	Sepsis SC5	53	hu-sep-CNAD-0053
Table 1	Sepsis SC7	55	hu-sep-CNAD-0055
Table 2	Sepsis JU2	59	hu-sep-CNAD-0059
Table 2	Sepsis JU4	61	hu-sep-CNAD-0061
Table 2	Sepsis JU11	68	hu-sep-CNAD-0068
Table 3	Sepsis J7	100	hu-sep-CNAD-0100
Table 3	Sepsis J15	108	hu-sep-CNAD-0108
Table 3	Sepsis J16	109	hu-sep-CNAD-0109
Table 3	Sepsis J17	110	hu-sep-CNAD-0110
Table 3	Sepsis J19	112	hu-sep-CNAD-0112
Table 3	Sepsis J21	114	hu-sep-CNAD-0114
Table 3	Sepsis J23	116	hu-sep-CNAD-0116
Table 3	Sepsis J36	129	hu-sep-CNAD-0129

Exemplary CNAs identified herein, which are internal reference regions, include SEQ ID NOs: 58-93. See Table 2 (FIG. 2). Exemplary primer pairs for amplifying each of SEQ ID NOs: 58-93 are also presented in Tables 1-3 (FIG. 1-3). Reference is made to the chromosomal locations to which each of these CNAs can be found in the human genome. Accordingly, larger polynucleotides comprising each of SEQ ID NOs: 58-93, respectively, can readily be determined via access to publicly available databases. Additional primers for amplifying each of SEQ ID NOs: 58-93, respectively, can be designed based on the availability of such additional sequence information.
Candidate internal reference regions (Table 2: SEQ ID NOs: 58-93) were evaluated to identify the ones that were most consistently represented across a set of sepsis and control samples. Given a candidate reference region, the differences in median Cq values of the regions between sepsis samples and control samples were calculated. The lesser the difference in the median Cq values, the higher the consistency of the region across sepsis and non-sepsis conditions, and therefore the more suitable the region as an internal reference region.
The three most consistent regions were selected as exemplary internal reference regions (SEQ ID NOs: 59, 61 and 68). Their sequences and primers used for amplification are listed in Table 2 in the corresponding rows of the regions.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 1, 6, 46, 50, 53, 55, 100, 109, 110, 114, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 1, 6, 46, 50, 53, 55, 59, 61, 68, 100, 109, 110, and 114 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 1, 2, 6, 30, 53, 55, 110, 112, 114, 116, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 1, 2, 6, 30, 53, 55, 59, 61, 68, 110, 112, 114, and 116 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 30, 31, 38, 44, 46, 50, 53, 55, 100, 129, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 30, 31, 38, 44, 46, 50, 53, 55, 59, 61, 68, 100, and 129 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 4, 5, 30, 31, 100, 108, 109, 110, 116, 129, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 4, 5, 30, 31, 59, 61, 68, 100, 108, 109, 110, 116, and 129 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 53, 55, 100, 108, 109, 110, 112, 114, 116, 129, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 53, 55, 59, 61, 68, 100, 108, 109, 110, 112, 114, 116, and 129 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 30, 31, 46, 55, 108, 110, 112, 114, 116, 129, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 30, 31, 46, 55, 59, 61, 68, 108, 110, 112, 114, 116, and 129 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 1, 2, 5, 46, 53, 100, 112, 114, 116, 129, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 1, 2, 5, 46, 53, 59, 61, 68, 100, 112, 114, 116, and 129 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 2, 4, 6, 31, 44, 100, 109, 110, 116, 129 and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 2, 4, 6, 31, 44, 59, 61, 68, 100, 109, 110, 116, and 129 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 5, 6, 30, 31, 44, 50, 55, 100, 110, 112, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 5, 6, 30, 31, 44, 50, 55, 59, 61, 68, 100, 110, and 112 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 2, 31, 38, 44, 46, 55, 109, 110, 112, 129, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 2, 31, 38, 44, 46, 55, 59, 61, 68, 109, 110, 112, and 129 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 4, 5, 6, 30, 38, 44, 53, 55, 108, 109, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 4, 5, 6, 30, 38, 44, 53, 55, 59, 61, 68, 108, and 109 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 31, 46, 55, 108, 114, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 31, 46, 55, 59, 61, 68, 108, and 114 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 100, 109, 112, 114, 116, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 59, 61, 68, 100, 109, 112, 114, and 116 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 31, 38, 44, 100, 108, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 31, 38, 44, 59, 61, 68, 100, and 108 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 1, 4, 5, 110, 112, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 1, 4, 5, 59, 61, 68, 110, and 112 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 5, 6, 44, 55, 109, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 5, 6, 44, 55, 59, 61, 68, and 109 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 1, 2, 5, 50, 53, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 1, 2, 5, 50, 53, 59, 61, and 68 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 4, 5, 6, 31, 38, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 4, 5, 6, 31, 38, 59, 61, and 68 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 1, 53, 100, 114, 116, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 1, 53, 59, 61, 68, 100, 114 and 116 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 5, 6, 30, 31, 38, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 5, 6, 30, 31, 38, 59, 61 and 68 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 44, 46, 50, 53, 55, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 44, 46, 50, 53, 55, 59, 61, and 68 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 109, 110, 112, 114, 116, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 59, 61, 68, 109, 110, 112, 114, and 116 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 4, 5, 114, 116, 119 and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 4, 5, 59, 61, 68, 114, 116, and 119 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 4, 6, 30, 100, 108 and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 4, 6, 30, 59, 61, 68, 100, and 108 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 38, 44, 109, 110, 112 and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 38, 44, 59, 61, 68, 109, 110, and 112 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 1, 2, 4, 5, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 1, 2, 4, 5, 59, 61, and 68 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 30, 53, 108, 109, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 30, 53, 59, 61, 68, 108, and 109 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 2, 109, 110, 116, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 2, 59, 61, 68, 109, 110, and 116 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 5, 6, 50, 53, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 5, 6, 50, 53, 59, 61, and 68 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 1, 31, 55, 108, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 1, 31, 55, 59, 61, 68, and 108 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 30, 38, 55, 100, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 30, 38, 55, 59, 61, 68, and 100 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 2, 4, 112, 114, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 2, 4, 59, 61, 68, 112, and 114 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 31, 110, 112, 114, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 31, 59, 61, 68, 110, 112, and 114 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 5, 31, 116, 129, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 5, 31, 59, 61, 68, 116, and 129 are presented in Tables 1-3.
An exemplary subset of SEQ ID NOs: set forth in Table 4 comprises SEQ ID NOs: 2, 4, 5, 6, and at least one of SEQ ID NOs: 59, 61, or 68. Primers for amplifying SEQ ID NOs: 2, 4, 5, 6, 59, 61, and 68 are presented in Tables 1-3.
Machine learning classification systems, such as, e.g., a support vector or neural network are utilized herein. The system utilized herein creates a multidimensional ‘map’ comprising basically all the markers (both sepsis and non-sepsis) and then when a sample is tested, it's position on the map it marked. After this, the system looks at the closest points and if they are sepsis, it will call the sample ‘sepsis’. If the closest points are not sepsis, it will call the sample ‘not sepsis’. In a particular embodiment, the system looks for a certain small number of neighboring samples (not the single closest one) in this virtual multidimensional space, where each sample is represented by a group of marker values on the sample. The assignment of the sample to sepsis/non-sepsis is accomplished by a majority vote of the known labels of the closest neighbors (e.g., 5 of them). If there are more sepsis samples in the neighborhood, the incoming sample is assigned to “sepsis”. If there are more non-sepsis samples in the neighborhood, the new sample is assigned to “non-sepsis”.
“Encode” refers to a polynucleotide “encoding” a polypeptide if, in its native state or when manipulated by methods well known to those skilled in the art, it can be transcribed and/or translated to produce the mRNA for the polypeptide and/or the polypeptide (or a fragment thereof). The anti-sense strand is the complement of such a nucleic acid, and the encoding sequence can be deduced therefrom.
“Array” or “microarray” refers to an ordered arrangement of hybridizable array elements on a substrate, such as a solid substrate (e.g., glass slide and the like) or a semi-solid substrate (e.g., nitrocellulose membrane and the like). In some embodiments, the array elements may be polynucleotide probes (e.g. oligonucleotide). Arrays may include DNA microarrays (including cDNA microarrays, oligonucleotide microarrays, SNP microarrays, etc.), protein microarrays, peptide microarrays, antibody microarrays, and the like.
“Amplification” or “amplifying” refers to the production of one or more copies of a reference nucleic acid sequence or its complement. Amplification may be linear or exponential (e.g., in a polymerase chain reaction (PCR)). A nucleic acid copy produced from amplification may not have perfect sequence complementarity or identity relative to the reference sequence. In some embodiments, the copies can include nucleotide analogs, including deoxyinosine, intentional sequence alterations (such as alterations introduced through a primer that is hybridizable, but not fully complementary, to the template), and/or sequence errors that occur during the amplification process.
The terms “expression” and “expression level”, in general, are used interchangeably and generally refer to the amount of a marker in a sample. “Expression” generally refers to the process by which information (e.g., gene-encoded and/or epigenetic) is converted into the structures present and operating in the cell. Therefore, as used herein, “expression” can refer to transcription into a polynucleotide (such as mRNA and the like), translation into a polypeptide, or even polynucleotide and/or polypeptide modifications (e.g., post-translational modification of a polypeptide and the like). Fragments of the transcribed polynucleotide, the translated polypeptide, or polynucleotide and/or polypeptide modifications (such as post-translational modification of a polypeptide and the like) will also be regarded as expressed whether they originate from a transcript generated by alternative splicing or a degraded transcript, or from a post-translational processing of the polypeptide (e.g., by proteolysis). “Expressed genes” include those that are transcribed into a polynucleotide as mRNA and then translated into a polypeptide, and also those that are transcribed into RNA but not translated into a polypeptide (such as transfer and ribosomal RNAs and the like).
An “isolated” nucleic acid refers to a nucleic acid molecule that has been separated from a component of its natural environment. An isolated nucleic acid includes a nucleic acid molecule contained in cells that ordinarily contain the nucleic acid molecule. The nucleic acid molecule may be present extrachromosomally or at a chromosomal location that is different from its natural location.
The term “sequencing” and its variants include obtaining sequence information from a strand of a nucleic acid molecule, typically by determining the identity of at least some nucleotides (including their nucleic acid components) within the nucleic acid molecule. The term sequencing may also refer to determining the order of nucleotides (base sequences) in a nucleic acid sample (e.g. DNA or RNA). Many techniques are available and known to a person skilled in the art, such as Sanger sequencing, high-throughput sequencing technologies (such as the GS FLX platform formerly offered by Roche Applied Science, Penzberg, Germany, based on pyro sequencing, or Illumina sequencing platforms, as offered by Illumina Inc., 5200 Illumina Way, San Diego, Calif. 92122, USA), and the like. High-throughput sequencing technologies refer to sequencing technologies having increased throughput as compared to traditional Sanger- and capillary-electrophoresis-based approaches (e.g., with the ability to generate hundreds of thousands or millions of relatively small sequence reads at a time). High throughput sequencing technologies include, but are not limited to, sequencing by synthesis, sequencing by ligation, pyrosequencing, sequencing by hybridization, and/or the like.
As used herein, “reactive” means the agent has affinity for, binds to, or is directed against a specific CNA. As further used herein, an “agent” includes a protein, polypeptide, peptide, nucleic acid (including DNA or RNA), antibody, Fab fragment, F(ab′)2 fragment, molecule, compound, antibiotic, drug, and any combinations thereof. A Fab fragment is a univalent antigen-binding fragment of an antibody, which is produced by papain digestion. A F(ab′)2 fragment is a divalent antigen-binding fragment of an antibody, which is produced by pepsin digestion. By way of example, the agent of the present invention can be labeled with a detectable marker. Agents that are reactive with CNAs can be identified by contacting the CNA with an agent of interest and assessing the ability of the agent to bind to the CNA.
In one embodiment of the present invention, the agent reactive with a sepsis biomarker is an antibody. Antibodies for use herein can be labeled with a detectable marker. Labeling of an antibody can be accomplished using one of a variety of labeling techniques, including peroxidase, chemiluminescent labels known in the art, and radioactive labels known in the art. The detectable marker of the present invention can be, for example, a nonradioactive or fluorescent marker, such as biotin, fluorescein (FITC), acridine, cholesterol, or carboxy-X-rhodamine (ROX), which can be detected using fluorescence and other imaging techniques readily known in the art. Alternatively, the detectable marker can be a radioactive marker, including, for example, a radioisotope. The radioisotope can be any isotope that emits detectable radiation, such as ³⁵S, ³²P, or ³H. Radioactivity emitted by the radioisotope can be detected by techniques well known in the art. For example, gamma emission from the radioisotope can be detected using gamma imaging techniques, particularly scintigraphic imaging. By way of example, the agent of the present invention is a high-affinity antibody labeled with a detectable marker.
Where the agent of the present invention is an antibody reactive with a sepsis biomarker, a biological sample taken from a mammal (e.g., a human) can be purified by passage through an affinity column which contains the antibody having affinity to the sepsis biomarker as a ligand attached to a solid support, such as an insoluble organic polymer in the form of a bead, gel, or plate. The antibody attached to the solid support can be used in the form of a column. Examples of suitable solid supports include, without limitation, agarose, cellulose, dextran, polyacrylamide, polystyrene, sepharose, and other insoluble organic polymers. The antibody can be further attached to the solid support through a spacer molecule, if desired. Appropriate binding conditions (e.g., temperature, pH, and salt concentration) can be readily determined by the skilled artisan. By way of example, the antibody can be attached to a sepharose column, such as Sepharose 4B.
Alternatively, a biological sample from a mammal (e.g., a human) can be assayed using hybridization analysis of nucleic acid extracted from the biological sample taken from the mammal (e.g., a human) to determine the presence of a sepsis biomarker, such as a CNA. This method also can be conducted by performing a Southern blot analysis of DNA using at least one nucleic acid probe which hybridizes to CNAs (including amplified CNAs). The nucleic acid probes described herein can be prepared by a variety of techniques known to those skilled in the art, including, without limitation, the following: restriction enzyme digestion of nucleic acid; and automated synthesis of oligonucleotides having sequences which correspond to selected portions of the nucleotide sequence of the sepsis biomarker, using commercially-available oligonucleotide synthesizers.
The nucleic acid probes used herein can be DNA or RNA, and can vary in length from about 5-20 nucleotides or 10-20 nucleotides to the entire length of the nucleic acid encoding for a sepsis biomarker. In some embodiments, the nucleic acid probes are oligonucleotides. The nucleic acid used in the probes can be derived from mammalian polynucleotide sequence complementary to the sepsis biomarker. In addition, the nucleic acid probes of the present invention can be labeled with one or more detectable markers. Labeling of the nucleic acid probes can be accomplished using one of a number of methods known in the art (e.g., nick translation, end labeling, fill-in end labeling, polynucleotide kinase exchange reaction, random priming, SP6 polymerase (for riboprobe preparation)) along with one of a variety of labels (e.g., radioactive labels, such as ³⁵S, ³²P, or ³H, or nonradioactive labels, such as biotin, fluorescein (FITC), acridine, cholesterol, or carboxy-X-rhodamine (ROX)). In some embodiments, these nucleic acid probes are used in an array or microarray.
In addition, the present invention provides a method of determining whether a human has sepsis, but is asymptomatic, or has already developed sepsis and has symptoms thereof. The method includes analyzing a biological sample of the human for the presence of at least one sepsis biomarker, and optionally, further recommending a corroborative test for sepsis if the at least one sepsis biomarker is present in the biological sample. In some embodiments, the corroborative test includes ELISA, immunohistochemistry, and Western Blot/immunoblot or a combination of more than one of any of the foregoing.
In the methods described herein, the step of analyzing a biological sample may optionally include obtaining the sample from the human; isolating nucleic acid from the sample; amplifying the isolated nucleic acid using primers that are specific for or capable of amplifying a sequence corresponding to a sepsis CNA biomarker; and sequencing the amplified nucleic acid. In some embodiments, the isolated nucleic acid includes genomic DNA, mRNA, and/or cDNA obtained from mRNA. In some embodiments, the step of determining representation of the at least one sepsis CNA marker includes use of at least one of a PCR-based detection method and a hybridization-based method. In some embodiments, the step of determining representation of the at least sepsis CNA marker includes an immunohistochemical analysis. In some embodiments, an array or a microarray is used for identifying the sepsis biomarker.
The biological sample can be assayed for expression of sepsis biomarkers in vitro or in vivo. In addition, the biological sample can be assayed for expression of sepsis biomarkers using all of the various assays and methods of detection and quantification described above.
The discovery that certain CNAs constitute sepsis biomarkers provides compositions and methods for identifying a human having early stage sepsis (e.g., pre-symptomatic sepsis), and presents the potential for commercial application in the form of a test for the diagnosis of sepsis and kits including same. The development of such a test or kit would provide general screening procedures; these procedures could assist in the early detection and diagnosis of sepsis in human subjects. Accordingly, the present invention further provides a kit for use as an assay of sepsis, comprising at least one agent reactive with a sepsis biomarker. The agent can be any of those described above, and can be used in any of the above-described assays or methods for detecting sepsis biomarkers.
Oligonucleotides complementary to a sepsis CNA biomarker can be designed based on the nucleotide sequence of the particular CNA sepsis biomarker. A nucleotide sequence complementary to the selected partial sequence of the sepsis CNA biomarker can, e.g., be chemically synthesized using one of a variety of techniques known to those skilled in the art, including, without limitation, automated synthesis of oligonucleotides having sequences which correspond to a partial sequence of the sepsis CNA biomarker nucleotide sequence, or a variation sequence thereof, using commercially-available oligonucleotide synthesizers.
The present invention also provides the use of an oligonucleotide capable of identifying at least one sepsis CNA biomarker to determine the representation of same in a human. The oligonucleotide can be labelled with a detectable marker, such as a radioactive marker, fluorescent marker, the like, or a combination of any of the foregoing.
Serum from healthy individuals (controls) and diseased patients (i.e. sepsis patients) was harvested and initially stored at −80 degrees Celsius. Total DNA was extracted from the serum samples using the High Pure Viral Nucleic Acid Kit (Roche Applied Science; Cat. No. 11858874001). The DNA was amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma; Cat. No. WGA4-500RXN) and purified using the GenElute™ PCR Clean-Up Kit (Sigma, Cat. No. NA1020-1KT). High-throughput paired-end DNA sequencing was performed by SEQ-IT Kaiserslautern Sequencing facility on NextSeq 500 sequencer and SEQ-IT machines. The resulting sequence reads were mapped to the human genome. Using an in-house Bioinformatics pipeline, which was established on the high-performance Bioinformatics infrastructure at the Institute of Computational Biotechnology at the Technical University of Graz, Austria, the present inventors have identified DNA motifs, which were present at different read count numbers in diseased humans, when compared to controls. The motifs identified are the result of the host response (i.e., the response of the human body to sepsis). The DNA motifs identified were used as targets for the development of a real-time Polymerase-Chain Reaction (RT-PCR) assay. In addition to the motifs, which are present at different levels in healthy controls and sepsis patients (markers; SEQ ID NOs: 1-57 or 94-148), motifs which were present at the same level in healthy and diseased humans were also identified to allow the normalization of the results (SEQ ID NOs: 58-93). The RT-PCR-evaluated motifs, which could be used to discriminate in a statistically significant manner between healthy controls and sepsis patients, stand-alone, or in combination with each other, are the subject basis for assays described herein.
In a particular embodiment, the Illumina sequences were analyzed using a genome assembly/mapping bioinformatics processing method. The cleaned sequence reads were mapped to the human genome using a fast mapper, genomic hotspots for sepsis were identified, the reads were comprehensively mapped to the identified hotspots, and a gene search was conducted in the hotspot region to correlate the reads with a gene. Reads that did not map to the genome were assembled to generate clusters and then analyzed using the same procedures used for the hotspots.
In an embodiment of an Illumina sequence analysis method, CNA libraries are obtained from a blood sample collection and these libraries are sequenced in an Illumina sequencing operation. After the sequencing operation, the method proceeds to an operation step, where the processing unit stores the output of the Illumina sequencing in a text-based file format, for example, a FASTQ format. It is understood that the output of the Illumina sequencing can also be stored in other file formats, such as, for example, SAM or BAM formats. The sequencing files are assembled with a reference genome to determine genome locations with significant counts of exclusively at risk or normal (not at risk) reads.
The results of the alignment are then processed. In some embodiments, the results of the alignment process are outputted in a text-based file format, such as a SAM format. A SAM formatted file is a tab-delimited text file that contains sequence alignment data. In such embodiments, the processing unit converts the SAM format to a BAM format, which is a binary version of the SAM formatted file. In other examples, the alignment process outputs a BAM formatted file, and thus, the conversion step is skipped. Preparation for and creation of an index file associated with the BAM formatted file is then created. The index file creation process may include categorizing by adding sample names as read groups, sorting, and/or merging.
The created index file and the BAM formatted file is further processed by a processing unit. In particular, processing includes reviewing the alignments and extracting the alignments, which have sufficient coverage for each contiguous sequence (=contig) of the reference genome. In an embodiment, the alignment parameters comprise a bucket size of 25 and a minimum coverage of 5, although it is understood that the bucket size and minimum coverage value may differ in alternate embodiments. Control regions and at risk regions having 50% or more proportion are extracted and compared to determine overlaps. In some embodiments, these regions are stored in a database associated with the processing unit for later retrieval and/or review. Next, the extracted control regions are subtracted from the at risk regions so that only the at risk regions remain, thereby providing sequence reads that are present in only at risk regions. In an embodiment, the control filtering parameters comprise a minimum subjects value of 3 and a minimum proportion value of 0.5, although it is understood that these values may differ in alternate embodiments.
In some embodiments, not all of the sequences are aligned. In such examples, the unaligned sequences are collected and may be stored in the database for later retrieval and/or review. In an embodiment, the unaligned sequences are aligned against other references, such as viral references, to determine if any alignments exist. If alignments exist, the sequences may be stored in the database for later retrieval and alignment with new viruses, as desired.
In an embodiment, analysis of Illumina sequencing reads can be achieved using a TimeLogic® Decypher® biocomputing platform (Active Motif, Carlsbad, Calif.) and multiple CPU servers at the sequencing center.
Sequence variability of the identified CNA motifs specific to sepsis risk was then analyzed in a sampling of different humans through PCR and Sanger sequencing of the PCR products to determine if the identified CNA motifs are capable of detecting sepsis risk generally. In healthy humans, it has been shown that approximately 97% of CNA sequences are of genomic origin [Beck et al., 2009, Clin Chem., 55(4):730-8].
Arrays comprising one of more polynucleotides of the disclosure, PCR primers and/or probes for amplifying and/or detecting polynucleotides (CNAs) described herein, and methods for detecting risk for developing sepsis comprising an array or PCR primers and/or probes are encompassed herein.
One of more polynucleotide sequences of the disclosure can be incorporated onto a sequence array, such as a biochip, DNA chip, BiofireDX filmarray and other filmarrays, microarray, macroarray, and the like, for screening, e.g., serum separated from whole blood from humans for sepsis risk. Alternatively, CNAs can be extracted from the sample for screening on the array. Arrays are generally solid supports upon which a collection of polynucleotides and/or primers and/or probes are placed at defined locations on the array, either by spotting, printing, or direct synthesis. The array can include probes corresponding to one or more of the polynucleotides described herein (e.g., at least one of SEQ ID NOs: 1-57 or 94-148 and/or primers and/or probes for amplifying and/or detecting one or more polynucleotides of SEQ ID NOs: 1-57 or 94-148 and at least one of SEQ ID NOs: 59, 61, or 68 and/or primers and/or probes for amplifying and/or detecting one or more polynucleotides of SEQ ID NOs: 59, 61, or 68).
The underlying principle of arrays is base pairing or hybridization i.e., A-T and G-C for DNA, and A-U and G-C for RNA. A sample from a mammal (e.g., a human) is allowed to hybridize with the polynucleotides and/or primers and/or probes on the array providing an expression profile/pattern of CNA. The CNA expression pattern of sepsis-specific sequences can be used to determine if a human has early stage sepsis. The array can be prepared by any method known in the art. In some embodiments, a microarray is prepared generally as disclosed in U.S. Pat. No. 7,655,397, the entirety of which is hereby incorporated by reference.
In some embodiments, the array comprises at least 2 polynucleotides selected from polynucleotides comprising or consisting of SEQ ID NOs: 1-57 or 94-148 or primers or probes specific for at least 2 of SEQ ID NOs: 1-57 or 94-148. In some embodiments, the array comprises at least 4 polynucleotides selected from polynucleotides comprising or consisting of SEQ ID NOs: 1-57 or 94-148 or primers or probes specific for at least 4 of SEQ ID NOs: 1-57 or 94-148. In another embodiment, the array comprises at least 5 polynucleotides selected from the polynucleotides comprising or consisting of SEQ ID NOs: 1-57 or 94-148 or primers or probes specific for at least 5 of SEQ ID NOs: 1-57 or 94-148. In another embodiment, the array comprises at least 10 polynucleotides selected from the polynucleotides comprising or consisting of SEQ ID NOs: 1-57 or 94-148 or primers or probes specific for at least 10 of SEQ ID NOs: 1-57 or 94-148. In some embodiments, the array comprises the 24 polynucleotides listed in Table 4 and/or primers and/or probes specific for the 24 polynucleotides listed in Table 4. The array generally includes many copies of the selected polynucleotides to facilitate detection. In some embodiments, the array comprises a million or more copies of each of the selected polynucleotides.
In a particular embodiment, the array comprises or consists of SEQ ID NOs: listed in Table 4 or primers or probes specific for the SEQ ID NOs: listed in Table 4. Also encompassed herein is an array comprising or consisting of subsets of SEQ ID NOs: listed in Table 4 or primers or probes specific for these SEQ ID NOs: as set forth herein.
Probes for detecting polynucleotides described herein can be designed and prepared using conventional methods. Software for modeling and designing probes, including determining hybridization and annealing conditions, for detecting a specific polynucleotide sequence are publically available, and include for example LightCycler® Probe Design Software (Roche Applied Science), Primer3 (Simgene), and FastPCR (PrimerDigital). See also techniques described by Illumina (Illumina Inc., 5200 Illumina Way, San Diego, Calif. 92122, USA).
The array can include positive indicator for sepsis sequences and/or probes for detecting same and negative and/or positive control sequences and/or probes.
Polynucleotides described herein can be amplified and/or detected via PCR, including but not limited to real-time PCR, multiplex PCR, nested PCR, solid phase PCR, miniprimer PCR, and the like. Primers and probes for amplifying and/or detecting polynucleotides described herein can be designed and prepared using conventional methods. Software for modeling and designing primers and probes, including determining hybridization, melting, annealing, and/or extensions conditions, for amplifying and/or detecting a specific polynucleotide sequence are publicly available, and include for example LightCycler® Probe Design Software (Roche Applied Science), Primer3 (Simgene), and FastPCR (PrimerDigital). See also techniques described by Illumina (Illumina Inc., 5200 Illumina Way, San Diego, Calif. 92122, USA). PCR conditions generally include the presence of four different nucleotide bases (adenosine, cytidine, guanosine, thymidine/uridine) and at least one polymerization-inducing agent such as a reverse transcriptase or a DNA polymerase. The primers are generally present in a suitable buffer, which may include constituents, which are co-factors or affect conditions such as pH and the like at various suitable temperatures. The primers are preferably single-strand nucleotide sequences, such that amplification efficiency of the desired polynucleotide is optimized. Double-stranded nucleotide sequences can also be utilized. The primers are typically at least about 15 nucleotides. In some embodiments, the primers can have a length of from about 15 to about 30, about 15 to about 50, about 15 to about 75, about 15 to about 100, or about 15 to about 500 nucleotides.
In some embodiments, primer sets are designed to amplify one or more of the sepsis-specific polynucleotides comprising or consisting of SEQ ID NOs: 1-57 or 94-148 and then the PCR products of the primer sets are screened for sepsis-specific sequences on an array as described herein.
Diagnostic kits comprising one or more primer pairs, and optional probes, for amplifying and detecting one or more polynucleotides described herein are also provided. The kit can optionally include nucleotide bases (adenosine, cytidine, guanosine, thymidine/uridine) and at least one polymerization-inducing agent such as a reverse transcriptase or a DNA polymerase. The kit can optionally include a suitable primer buffer, which may include constituents which are co-factors or affect conditions such as pH and the like at various suitable temperatures. The kit can optionally include an array as described herein.
The primers provided in the diagnostic kit are generally provided in pairs (forward primer and reverse primer) for amplifying/detecting a specific polynucleotide sequence. These primers can be used to amplify and detect CNAs in blood serum from humans, or any other appropriate biological sample from humans that may contain CNAs. Alternatively, CNAs can be extracted from the sample and then amplified by PCR using a diagnostic kit of the disclosure. The CNA expression pattern of sepsis-specific sequences detected by the diagnostic kit can be used to determine if a human has early stage sepsis even at a stage wherein no clinical symptoms of sepsis are apparent
In addition to polynucleotide sequence specific primer pairs, labeled probes specific for each of the CNAs may be included in kits described herein. Labeled probes and use thereof in the context of, for example, multiplex qPCR provides for enhanced specificity of detection.
In some embodiments, the kit comprises primers for amplifying at least 2 polynucleotides selected from the polynucleotides comprising or consisting of SEQ ID NOs: 1-57 or 94-148, and optionally one or more probes for detecting the amplified product. In some embodiments, the kit comprises primers for amplifying at least 4 polynucleotides selected from the polynucleotides comprising or consisting of SEQ ID NOs: 1-57 or 94-148, and optionally one or more probes for detecting the amplified product. In another embodiment, the kit comprises primers for amplifying at least 5 polynucleotides selected from the polynucleotides comprising or consisting of SEQ ID NOs: 1-57 or 94-148, and optionally one or more probes for detecting the amplified product. In another embodiment, the kit comprises primers for amplifying at least 10 polynucleotides selected from the polynucleotides comprising or consisting of SEQ ID NOs: 1-57 or 94-148, and optionally one or more probes for detecting the amplified product. In some embodiments, the kit comprises primers for amplifying the 24 polynucleotides listed in Table 4, and optionally one or more probes for detecting the amplified product.
In a particular embodiment, the kit comprises or consists of SEQ ID NOs: listed in Table 4 and/or primers and/or probes specific for the SEQ ID NOs: listed in Table 4. Also encompassed herein are kits comprising or consisting of subsets of SEQ ID NOs: listed in Table 4 and/or primers and/or probes specific for these SEQ ID NOs: as set forth herein.
The present invention is described in the following Examples, which are set forth to aid in an understanding of the invention, and should not be construed to limit in any way the scope of the invention as defined in the claims which follow thereafter.

EXAMPLES

Example 1—Identification of Sepsis-Associated Polynucleotides in CNAs

Serum from healthy individuals (controls) and diseased patients (e.g., sepsis patients who were symptomatic or sepsis patients with early stage disease, but were asymptomatic) was harvested and total DNA was extracted from the serum samples. DNA was amplified and purified from the serum samples as described herein above. High-throughput paired-end DNA sequencing was performed and the resulting sequence reads were mapped to the human genome. Bioinformatics was used as described herein to identify DNA motifs that were present at distinctively high or low read count numbers in diseased humans, when compared to controls, corresponding to motifs that are over- and under-represented in sepsis patients. See, for example, Tables 1 and 3, which present motifs (Sequences) that are under-represented in sepsis patients (Table 1) or over-represented in sepsis patients (Table 3). The motifs identified reflect the host response to sepsis (i.e., the response of the human body to sepsis). The DNA motifs thus identified were used as targets for the development of a real-time Polymerase-Chain Reaction (RT-PCR) assay. In addition to the motifs, which are present at distinctively different levels in healthy controls and sepsis patients, motifs that were present at a highly similar level in healthy and diseased humans were also identified to allow for the normalization of the results. See, for example, Sequences presented in Table 2. The RT-PCR-evaluated motifs, which are used to discriminate between healthy controls and sepsis patients in a statistically significant manner, when evaluated alone or in combination with other motifs, are the subject basis for assays described herein.
All publications mentioned herein are hereby incorporated by reference in their entireties. While the foregoing invention has been described in some detail for purposes of clarity and understanding, it will be appreciated by one skilled in the art from a reading of the disclosure that various changes in form and detail can be made without departing from the true scope of the invention in the appended claims.
Specific examples of methods and kits have been described herein for purposes of illustration. These are only examples. The technology provided herein can be applied to systems other than the example systems described above. Many alterations, modifications, additions, omissions, and permutations are possible within the practice of this invention. This invention includes variations on described embodiments that would be apparent to the skilled addressee, including variations obtained by: replacing features, elements and/or acts with equivalent features, elements and/or acts; mixing and matching of features, elements and/or acts from different embodiments; combining features, elements and/or acts from embodiments as described herein with features, elements and/or acts of other technology; and/or omitting combining features, elements and/or acts from described embodiments.
The embodiments of the invention described above are intended to be exemplary only. Those skilled in this art will understand that various modifications of detail may be made to these embodiments, all of which come within the scope of the invention.

Claims

1. A method comprising

administering to a human identified as having sepsis a therapeutically effective amount of at least one agent used to treat sepsis,

wherein the human is identified as having sepsis by

analyzing a biological sample isolated from the human for over-representation or under-representation of at least one polynucleotide relative to an internal reference region, wherein the at least one polynucleotide comprises any one of SEQ ID NOs: 1-57 or 94-148 and

wherein the over-representation or under-representation of the at least one polynucleotide in the biological sample is indicative of sepsis, thereby identifying the human as having sepsis.

2. The method of claim 1, wherein the at least one polynucleotide comprising any one of SEQ ID NOs: 1-57 or 94-148 over-represented or under-represented relative to the internal reference region is at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, at least twenty, at least twenty-one, at least twenty-two, at least twenty-three, or at least twenty-four of the polynucleotides comprising any one of SEQ ID NOs: 1-57 or 94-148.

3. The method of claim 1, wherein the biological sample is blood, a product derived from blood, or a fraction derived from blood.

4. The method of claim 1, wherein the internal reference region comprises at least one polynucleotide comprising at least one of SEQ ID NOs: 59, 61, or 68.

5. The method of claim 1, wherein detecting the over-representation or under-representation of the at least one polynucleotide relative to an internal reference region comprises at least one of a polymerase chain reaction (PCR)-based detection method, a hybridization-based method, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), solid-phase enzyme immunoassay (EIA), mass spectrometry, or microarray analysis.

6. The method of claim 5, wherein the PCR-based detection method is performed using at least one primer pair, wherein each primer pair of the at least one primer pair is specific for any one of SEQ ID NOs: 1-57 or 94-148, and a primer pair specific for at least one of SEQ ID NOs: 59, 61, or 68.

7. The method of claim 6, wherein the primer pair specific for any one of SEQ ID NOs: 1-57 or 94-148 and the primer pair specific for at least one of SEQ ID NOs: 59, 61, or 68 is any one of the primer pairs presented in Tables 1-3.

8. The method of claim 7, further comprising sequencing amplification products corresponding to any one of SEQ ID NOs: 1-57 or 94-148 at least one of SEQ ID NOs: 59, 61, or 68 generated by the PCR-based detection method.

9. The method of claim 1, wherein the at least one polynucleotides comprise circulating nucleic acids.

10. The method of claim 1, wherein the at least one agent used to treat sepsis comprises at least one of an antibiotic, anti-fungal agent, anti-viral agent, anti-parasitic agent, or fluids suitable for intravenous administration.

11. A primer comprising a manmade nucleotide sequence that binds specifically to a polynucleotide comprising any one of the SEQ ID NOs: listed in Table 4 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is any one of the polynucleotide primer sequences listed in Tables 1-3 or a variant thereof.

12. The primer of claim 11, wherein the variant of any one of the polynucleotide primer sequences listed in Tables 1-3 is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the polynucleotide sequences listed in Table 4.

13. The primer of claim 11, wherein the manmade tag is a detectable marker.

14. The primer of claim 11, the primer consisting essentially of or consisting of a manmade nucleotide sequence that binds specifically to a polynucleotide of any one of the SEQ ID NOs: listed in Table 4 and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is any one of the polynucleotide primer sequences listed in Tables 1-3 or a variant thereof and at least one manmade tag conjugated thereto, wherein the manmade nucleotide sequence is any one of the polynucleotide primer sequences listed in Tables 1-3 or a variant thereof.

15. The polynucleotide primer sequence of claim 14, wherein the variant of any one of the polynucleotide primer sequences listed in Tables 1-3 is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the polynucleotide primer sequences listed in Tables 1-3.

16. The primer of claim 14, wherein the manmade tag is a detectable marker.

17. A kit for detecting sepsis in a human comprising at least one primer pair of claim 11 and instructions for use thereof.

18. The kit of claim 17, wherein the at least one primer pair comprises four primer pairs and wherein each primer pair of the four primer pairs specifically amplifies a different polynucleotide comprising any one of the SEQ ID NOs: listed in Table 4.