Cerebrospinal fluid assay
The present invention is directed to methods of isolating particles, such as nucleic acid-containing particles or microvesicles, from a biological sample and extracting nucleic acids therefrom, wherein the biological sample is cerebrospinal fluid. The present invention further provides methods for aiding diagnosis, prognosis, monitoring and evaluation of a disease or other medical condition in a subject by detecting a biomarker associated with a disease or medical condition thereof.
1. A method for diagnosis, prognosis, monitoring or therapy selection for a disease or medical condition of a subject, comprising the steps of:
a. obtaining a cerebrospinal fluid (CSF) sample from a subject;
b. processing the CSF sample to remove cells and cell debris and isolating microvesicles from the CSF sample, wherein the processing comprises
(i) pre-processing comprising one or more centrifugation steps at a speed in the range of 100-500 g, at a speed in the range of 2,000-200,000 g, or a combination thereof, one or more filtration steps using a filter having a size in the range of 0.1-1.0 μm, or a combination thereof
(ii) followed by isolating the microvesicles from the sample, wherein isolating comprises one or more centrifugation steps, size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, filtration concentration, immunoabsorbent capture, affinity purification, ion exchange chromatography, microfluidic separation, or combinations thereof;
c. extracting one or more nucleic acids from the microvesicles;
d. detecting a level of expression for a biomarker associated with a disease or medical condition in the extracted nucleic acids, and detecting a level of expression of a reference gene in the extracted nucleic acids, wherein the reference gene is a brain-associated gene; and
e. determining a normalized, relative expression level of the biomarker, wherein the relative expression level of the biomarker is a ratio between the level of biomarker expression to the level of reference gene expression,
wherein the subject is identified as suffering from, or being at an increased risk for, the disease or medical condition when the relative expression level of the biomarker is greater than or less than a cutoff level of biomarker expression, wherein the cutoff level of biomarker expression is a score based on a collective level of biomarker expression in a control group of subjects that are not suffering from the medical condition of the brain or wherein the cutoff level of biomarker expression is a score based on a collective level of biomarker expression in a control group of subjects that have been diagnosed with a low level or early stage of the disease or medical condition.
2. The method of claim 1 , wherein the reference gene is U6.
3. The method of claim 1 , wherein the biomarker is:
a. a species of nucleic acid;
b. the level of expression of a nucleic acid;
c. a nucleic acid variant; or
d. a combination thereof.
4. The method of claim 1 , wherein the biomarker is messenger RNA, microRNA, siRNA or shRNA.
5. The method of claim 1 , wherein the biomarker is associated with the brain.
6. The method of claim 1 , wherein the biomarker is associated with glioblastoma or other brain cancer.
7. The method of claim 1 , wherein the biomarker is a nucleic acid corresponding to an EGFR variant.
8. The method of claim 7 , wherein the EGFR variant is EGFRvIII.
9. The method of claim 1 , wherein the biomarker is associated with Alzheimer's disease or other neurodegenerative disease.
10. The method of claim 1 , wherein the biomarker is a nucleic acid corresponding to APP, Aβ42, BACE-1, Tau or a combination thereof.
11. The method of claim 1 , wherein the subject or patient is a human subject or patient.
12. The method of claim 11 , wherein the subject or patient is a pediatric subject or patient.
13. The method of claim 1 , wherein disease or other medical condition is a brain cancer or a neurodegenerative disease.
14. The method of claim 13 , wherein the brain cancer is glioblastoma.
15. The method of claim 13 , wherein the neurodegenerative disease is Alzheimer's disease.
16. The method of claim 1 , wherein the biomarker is a nucleic acid and the method further comprises amplification of the nucleic acid.
17. The method of claim 1 , wherein the detecting in step d) is performed by microarray analysis, PCR, hybridization with allele-specific probes, enzymatic mutation detection, ligation chain reaction (LCR), oligonucleotide ligation assay (OLA), flow-cytometric heteroduplex analysis, chemical cleavage of mismatches, mass spectrometry, nucleic acid sequencing, single strange conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), restriction fragment polymorphisms, serial analysis of gene expression (SAGE) or combinations thereof.
18. The method of claim 1 , wherein the CSF sample is subjected to storage in a 4° C. environment prior to processing.
19. The method of claim 1 , wherein the CSF sample is subjected to storage in a less than −70° C. environment prior to processing.
20. A method for diagnosis, prognosis, monitoring or therapy selection for a disease or medical condition of a subject, comprising the steps of:
a. obtaining a cerebrospinal fluid (CSF) sample from a subject;
b. processing the CSF sample to remove cells and cell debris and isolating microvesicles from the CSF sample, wherein the processing comprises
(i) pre-processing comprising one or more centrifugation steps at a speed in the range of 100-500 g, at a speed in the range of 2,000-200,000 g, or a combination thereof, one or more filtration steps using a filter having a size in the range of 0.1-1.0 μm, or a combination thereof
(ii) followed by isolating the microvesicles from the sample, wherein isolating comprises one or more centrifugation steps, size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, filtration concentration, immunoabsorbent capture, affinity purification, ion exchange chromatography, microfluidic separation, or combinations thereof;
c. extracting one or more nucleic acids from the microvesicles;
d. detecting a level of expression for a biomarker associated with a disease or medical condition in the extracted nucleic acids, and detecting a level of expression of a reference gene in the extracted nucleic acids, wherein the reference gene is a brain-associated gene; and
e. determining a normalized, relative expression level of the biomarker, wherein the relative expression level of the biomarker is a ratio between the level of biomarker expression to the level of reference gene expression,
wherein the subject is identified as suffering from, or being at an increased risk for, the disease or medical condition when the relative expression level of the biomarker is greater than or less than a cutoff level of biomarker expression or wherein the cutoff level of biomarker expression is a score based on a collective level of biomarker expression in a control group of subjects that have been diagnosed with a low level or early stage of the disease or medical condition.