WO2011031877A1 - Use of microvesicles in analyzing nucleic acid profiles - Google Patents

Use of microvesicles in analyzing nucleic acid profiles Download PDF

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Publication number
WO2011031877A1
WO2011031877A1 PCT/US2010/048293 US2010048293W WO2011031877A1 WO 2011031877 A1 WO2011031877 A1 WO 2011031877A1 US 2010048293 W US2010048293 W US 2010048293W WO 2011031877 A1 WO2011031877 A1 WO 2011031877A1
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Prior art keywords
transcripts
rna transcripts
profile
rna
analysis
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PCT/US2010/048293
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French (fr)
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WO2011031877A9 (en
Inventor
Mikkel Noerholm
Johan Karl Olov SKOG
Xandra O. Breakefield
Bob Carter
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The General Hospital Corporation
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Priority to US13/395,284 priority Critical patent/US20130040833A1/en
Priority to EP10816090.4A priority patent/EP2475988B1/en
Priority to EP18199345.2A priority patent/EP3461912B1/en
Publication of WO2011031877A1 publication Critical patent/WO2011031877A1/en
Priority to US14/792,212 priority patent/US10407728B2/en
Publication of WO2011031877A9 publication Critical patent/WO2011031877A9/en
Priority to US16/520,130 priority patent/US11519036B2/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to the general fields of nucleic acid analysis in human or other animal subjects, particularly the profiling of nucleic acids from a biological sample, and in particular, from micro vesicles.
  • Cancer molecular diagnostics is becoming increasingly important with the accumulating knowledge of the molecular mechanisms underlying various types of cancers and the implications for diagnosis, treatment selection and prognosis.
  • PBMC Peripheral Blood Mononuclear Cells
  • CTC Circulating Tumor Cells
  • the present invention provides genetic profiles associated with biological conditions and methods of applying these profiles in evaluating the biological conditions.
  • the present invention is directed to a profile of one or more RNA transcripts obtained from microvesicles.
  • the one or more RNA transcripts are selected from those listed in Tables 1-20.
  • the microvesicles from which the profile is obtained are isolated from a bodily fluid from a subject.
  • the bodily fluid may be blood, serum, plasma or urine.
  • the subject is a human subject.
  • the human subject is a brain cancer patient such as a glioblastoma patient.
  • the profile is obtained through analyzing RNA transcripts obtained from microvesicles.
  • the analysis of RNA transcripts is performed by a method such as microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination of these above methods.
  • the analysis includes an additional step of data analysis.
  • the data analysis can be accomplished with Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis, Binary Analysis, Cox Proportional Hazards Analysis, Support Vector Machines and Recursive Feature Elimination (SVM-RFE), Classification to Nearest Centroid, Evidence-based Analysis, or a combination of the above methods.
  • the profile obtained from microvesicles is a profile of the one or more RNA transcripts selected from any one of the Tables 1-20. In yet another embodiment, the profile from microvesicles is a profile of each of the RNA transcripts listed in any one of the Tables 1-20.
  • the present invention refers to a method of aiding diagnosis, prognosis or therapy treatment planning for a subject, comprising the steps of: a) isolating microvesicles from a subject; b) measuring the expression level of one or more RNA transcripts extracted from the isolated microvesicles; c) determining a profile of the one or more RNA transcripts based on the expression level; and d) comparing the profile to a reference profile to aid diagnosis, prognosis or therapy treatment planning for the subject.
  • the microvesicles used in the method are isolated from a bodily fluid from the subject.
  • the bodily fluid may be blood, serum, plasma or urine.
  • the subject is a human subject.
  • the human subject is a brain cancer patient such as a glioblastoma patient.
  • the step (b) in the method is accomplished with a microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination of the above methods.
  • the step (c) in the method includes an additional step of data analysis.
  • the data analysis can be accomplished with Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis, Binary Analysis, Cox Proportional Hazards Analysis, Support Vector Machines and Recursive Feature Elimination (SVM-RFE), Classification to Nearest Centroid, Evidence-based Analysis, or a combination of the above methods.
  • RNA transcripts whose profiles are determined in are one or more RNA transcripts selected from those listed in Tables 1-20.
  • the RNA transcripts whose profiles are determined include one or more RNA transcripts selected from any one of the Tables 1- 20.
  • the RNA transcripts are all of the transcripts listed in any one of Tables 1-20.
  • the present invention refers to a method of preparing a personalized genetic profile report for a subject, comprising the steps of: (a) isolating microvesicles from a subject; (b) detecting or measuring one or more genetic aberrations within the isolated microvesicles; (c) determining one or more genetic profiles from the data obtained from steps (a) and (b); (d) optionally comparing the one or more genetic profiles to one or more reference profiles; and (e) creating a report summarizing the data obtained from steps (a) through (d) and optionally including diagnostic, prognostic or therapeutic treatment information.
  • step (b) comprises the quantitative measurement of one or more nucleic acids within the isolated microvesicles and step (c) comprises the determination of one or more quantitative nucleic acid profiles.
  • the one or more nucleic acids are RNA transcripts selected from Tables 1-20.
  • the one or more nucleic acids are RNA transcripts selected from any one of Tables 1- 20.
  • one or more nucleic acids comprise each of the RNA transcripts in any one of the Tables 1-20.
  • the present invention is a kit for genetic analysis of an exosome preparation from a body fluid sample from a subject, comprising, in a suitable container, one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from Tables 1-20.
  • the kit includes one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from any one of Tables 1-20.
  • the kit includes one or more reagents suitable for hybridizing to or amplifying each of the RNA transcripts in any one of Tables 1- 20.
  • the present invention is a custom-designed oligonucleotide microarray for genetic analysis of an exosome preparation from a body fluid sample from a subject, wherein the oligos on the array exclusively hybridize to one or more transcripts selected from any one of Tables 1-20.
  • the present invention is a method of identifying at least one potential biomarker for a disease or other medical condition, the method comprising: (a) isolating microvesicles from subjects having a disease or other medical condition of interest and from subjects who do not have the disease or other medical condition of interest; (b) measuring the expression level of a target RNA transcript extracted from the isolated microvesicles from each of the subjects; (c) comparing the measured levels of the target RNA transcript from each of the subjects; and (d) determining whether there is a statistically significant difference in the measured levels; wherein a determination resulting from step (d) of a statistically significant difference in the measured levels identifies the target RNA transcript and its corresponding gene as potential biomarkers for the disease or other medical condition.
  • the target RNA transcript is selected from Tables 1-20.
  • the present invention is a method of profiling genetic aberrations in a subject, comprising the steps of: (a) isolating microvesicles from a subject; (b) detecting or measuring one or more genetic aberrations within the isolated microvesicles; and (c) determining one or more genetic profiles from the data obtained from steps (a) and (b).
  • step (b) comprises the quantitative measurement of one or more nucleic acids within the isolated microvesicles
  • step (c) comprises the determination of one or more quantitative nucleic acid profiles.
  • the one or more nucleic acids are RNA transcripts selected from Tables 1-20.
  • the one or more nucleic acids are RNA transcripts selected from any one of Tables 1- 20. In yet another further embodiment, the one or more nucleic acids comprise each of the RNA transcripts in any one of Tables 1-20. In any of the inventive methods, a step of enriching the isolated microvesicles for microvesicles originating from a specific cell type may be optionally included.
  • the present invention may be as defined in any one of the following numbered paragraphs.
  • RNA transcripts is performed by a method comprising microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination thereof.
  • the profile of paragraph 9 wherein the data analysis comprises Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis, Binary Analysis, Cox Proportional Hazards Analysis, Support Vector Machines and Recursive Feature Elimination (SVM-RFE), Classification to Nearest Centroid, Evidence-based Analysis, or a combination thereof.
  • the profile of paragraph 10 wherein the data analysis comprises Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, or a combination thereof.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 1.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 1.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 2.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 2.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 3.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 3.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 4.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 4.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 5.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 5.
  • the profile paragraph 1, wherein the one or more RNA transcripts are selected from Table 6.
  • the profile of paragraph 1, wherein the one or more RNAs transcripts comprise each of the transcripts in Table 6.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 7.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 7.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 8.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 8.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 9.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 9.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 10.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 10.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 11.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 11.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 12.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 12.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 13.
  • RNA transcripts comprise each of the transcripts in Table 13.
  • RNA transcript comprise each of the transcripts in Table 14.
  • RNA transcripts are selected from Table 15.
  • RNA transcripts comprise each of the transcripts in Table 15.
  • RNA transcripts are selected from Table 16.
  • RNA transcripts comprise each of the transcripts in Table 16.
  • RNA transcripts comprise each of the transcripts in Table 17.
  • RNA transcripts are selected from Table 18.
  • RNA transcripts comprise each of the transcripts in Table 18.
  • RNA transcripts are selected from Table 19.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 19.
  • the profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 20.
  • the profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 20.
  • a method of aiding diagnosis, prognosis or therapy treatment planning for a subject comprising: a. isolating microvesicles from a subject; b. measuring the expression level of one or more RNA transcripts extracted from the isolated microvesicles; c. determining a profile of the one or more RNA transcripts based on the
  • step (b) is performed by a method comprising microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination thereof.
  • step (c) performed by a method of data analysis.
  • RNA transcripts are selected from Tables 1-16.
  • the method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 1.
  • the method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 1.
  • the method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 2.
  • the method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 2.
  • the one or more RNA transcripts are selected from Table 3.
  • the method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 3.
  • the method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 4. 70.
  • the method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 4.
  • RNA transcripts comprise each of the transcripts in Table 6.
  • RNA transcripts comprise each of the transcripts in Table 7.
  • RNA transcripts comprise each of the transcripts in Table 8.
  • RNA transcripts comprise each of the transcripts in Table 9.
  • RNA transcripts comprise each of the transcripts in Table 10.
  • RNA transcripts are selected from Table 11.
  • RNA transcripts comprise each of the transcripts in Table 11.
  • RNA transcripts comprise each of the transcripts in Table 12.
  • RNA transcripts comprise each of the transcripts from Table 14.
  • RNA transcripts comprise each of the transcripts from Table 15.
  • RNA transcripts comprise each of the transcripts from Table 16.
  • RNA transcripts are selected from Table 17.
  • the one or more RNA transcripts comprise each of the transcripts from Table 17.
  • RNA transcripts comprise each of the transcripts from Table 18.
  • RNA transcripts comprise each of the transcripts from Table 19.
  • RNA transcripts comprise each of the transcripts from Table 20.
  • a method of preparing a personalized genetic profile report for a subject comprising the steps of:
  • step (e) creating a report summarizing the data obtained from steps (a) through (d) and optionally including diagnostic, prognostic or therapeutic treatment information.
  • step (b) comprises the quantitative
  • step (c) comprises the determination of one or more quantitative nucleic acid profiles.
  • kits for genetic analysis of an exosome preparation from a body fluid sample from a subject comprising, in a suitable container, one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from Tables 1-20.
  • kit of paragraph 108 comprising one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from any one of Tables 1- 20.
  • kit of paragraph 108 comprising one or more reagents suitable for hybridizing to or amplifying each of the RNA transcripts in any one of Tables 1-20.
  • a method of identifying at least one potential biomarker for a disease or other medical condition comprising:
  • condition of interest and from subjects who do not have the disease or other medical condition of interest;
  • RNA transcript identifies the target RNA transcript and its corresponding gene as potential biomarkers for the disease or other medical condition, and wherein the target RNA transcript is selected from Tables 1- 20.
  • a method of profiling genetic aberrations in a subject comprising the steps of:
  • step (b) comprises the quantitative
  • step (c) comprises the determination of one or more quantitative nucleic acid profiles.
  • FIGURE 1A Heatmap and Clustering diagram illustrating microarray data showing gene expression profiles from exosomes isolated from serum samples from
  • GBM Glioblastoma
  • Ctrl non-Glioblastoma human subjects
  • the GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM 19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 5xl0 and with the log-median-ratio (i.e. the logarithm to the ratio between the median expression level of a given gene in GBMs and the same gene in Ctrls,
  • FIGURE IB A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 1A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 2A Heatmap and Clustering diagram illustrating microarray data showing gene expression profiles from exosomes isolated from serum samples from
  • GBM Glioblastoma
  • Ctrl non-Glioblastoma human subjects
  • the GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM 19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 5xl0 and with the log-median-ratio being at least "1" or above.
  • the genes included in the data set are listed in Table 2.
  • FIGURE 2B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 2A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 3A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM 13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 1x10° and with the log-median-ratio being at least "1" or above.
  • the genes included in the data set are listed in Table 3.
  • FIGURE 3B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 3A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 4A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • the GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 2xl0 ⁇ 6 .
  • the genes included in the data set are listed in Table 4.
  • FIGURE 4B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 4A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 5A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • the GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO "5 .
  • the genes included in the data set are listed in Table 5.
  • FIGURE 5B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 5A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 6A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO "4 and with the log-median-ratio being at least "0.8" or above, or being at least "-0.8” or below.
  • the genes included in the data set are listed in Table 6.
  • FIGURE 6B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 6A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 7A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO "5 and with the log-median-ratio being at least "0.585” or above, the log-median-ratio being at least "0.8” or above, or being at least "-0.585” or below.
  • the genes included in the data set are listed in Table 7.
  • FIGURE 7B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 7A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 8A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO "4 and with the log-median-ratio being at least "1" or above, or being at least or below.
  • the genes included in the data set are listed in Table 8.
  • FIGURE 8B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 8A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 9A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM 18, GBM 19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO "5 and with the log-median-ratio being below "0".
  • the genes included in the data set are listed in Table 9.
  • FIGURE 9B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 9A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 10A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO 5 and with the log-median-ratio being above "0".
  • the genes included in the data set are listed in Table 10.
  • FIGURE 10B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 10A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 11 A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM 19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, CtrB, Ctrl7 and Ctrl8.
  • the heatmap shown is a part of the heatmap showing the expression of the genes listed in Table 11. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 1x10 4 .
  • FIGURE 1 IB. A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 11A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 12A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO 3 and with the log-median-ratio being at least "1" or above, or being or below.
  • the genes included in the data set are listed in Table 12.
  • FIGURE 12B A plot showing the result of a Principle Component Analysis
  • FIGURE 13 A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, CtrB, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 0.05 and with the log- median-ratio being at least "1" or above, or being or below.
  • the genes included in the data set are listed in Table 13.
  • FIGURE 13B A plot showing the result of a Principle Component Analysis
  • FIGURE 14A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM Glioblastoma
  • Ctrl non-Glioblastoma human subjects
  • the GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM 13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8 are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 0.05 and with the log- median-ratio being at least "0.585" or above.
  • the genes included in the data set are listed in Table 14.
  • FIGURE 14B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 14A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 15 A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • FIGURE 15B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 15A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 16A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • the GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the heatmap shown is a part of the heatmap showing the expression of the genes listed in Table 16. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 0.001.
  • FIGURE 16B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 16A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 18 A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the heatmap shown is a part of the heatmap showing the expression of the genes listed in Table 17.
  • the expression levels in the GBM samples and in the control samples are significantly different with a p ⁇ 5xl0 ⁇ 2 and the log-median-ratio being at least "1" or above or being at least or below.
  • the p-values were corrected using Benjamin and Hochberg method.
  • FIGURE 18B A plot showing the result of a Principle Component Analysis
  • FIGURE 19A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • the GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the heatmap shows the expression of the genes listed in Table 18. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are
  • FIGURE 19B A plot showing the result of a Principle Component Analysis
  • FIGURE 20A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • the GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, Ctrl5, Ctrl7 and Ctrl8.
  • the heatmap shows the expression of the genes listed in Table 19. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are
  • FIGURE 20B A plot showing the result of a Principle Component Analysis
  • PCA performed on the data set of Figure 20A with the same samples, the same genes and the same inclusion criteria.
  • FIGURE 21A Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl).
  • GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM 13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20.
  • the control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, CtrB, Ctrl7 and Ctrl8.
  • the heatmap shown is a part of the heatmap showing the expression of the genes listed in Table 20.
  • the expression levels in the GBM samples and in the control samples are significantly different with a p ⁇ 5xl0 "2 and the log-median-ratio being at least "- 1.5" or below.
  • the p-values were corrected using Benjamin and Hochberg method.
  • FIGURE 21 B A plot showing the result of a Principle Component Analysis
  • Microvesicles are shed by eukaryotic cells, or budded off of the plasma membrane, to the exterior of the cell. These membrane vesicles are heterogeneous in size with diameters ranging from about 10 nm to about 5000 nm.
  • the small microvesicles (approximately 10 to 1000 nm, and more often approximately 30 to 200 nm in diameter) that are released by exocytosis of intracellular multivesicular bodies or by double inward budding of multivesicular bodies are referred to in the art as "exosomes.”
  • the compositions, methods and uses described herein are equally applicable to microvesicles of all sizes; preferably 30 to 800 nm; and more preferably 30 to 200 nm.
  • exosome also refers to protein complexes containing exoribonucleases which are involved in mRNA degradation and the processing of small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNA) (Liu et al., 2006; van Dijk et al., 2007).
  • snoRNAs small nucleolar RNAs
  • snRNAs small nuclear RNAs
  • rRNA ribosomal RNAs
  • Certain aspects of the present invention are based on the surprising finding that glioblastoma derived microvesicles can be isolated from the serum of glioblastoma patients (Skog et al., 2008). This is the first discovery of microvesicles derived from cells in the brain, present in a bodily fluid of a subject. Prior to this discovery it was not known whether glioblastoma cells produced microvesicles or whether such microvesicles could cross the blood brain barrier into the rest of the body. These microvesicles were found to contain mutant mRNA associated with tumor cells (Skog et al., 2008).
  • microRNAs which were found to be abundant in glioblastomas (Skog et al., 2008). Glioblastoma-derived microvesicles were also found to potently promote angiogenic features in primary human brain microvascular endothelial cells (HBMVEC) in culture. This angiogenic effect was mediated at least in part through angiogenic proteins present in the microvesicles (Skog et al., 2008).
  • the nucleic acids found within these microvesicles, as well as other contents of the microvesicles such as angiogenic proteins, can be used as valuable biomarkers for tumor diagnosis, characterization and prognosis by providing a genetic profile. Contents within these microvesicles can also be used to monitor tumor progression over time by analyzing if other mutations are acquired during tumor progression as well as if the levels of certain mutations or gene expression increase or decrease over time or over a course of treatment.
  • Certain aspects of the present invention are based on another finding that most of the extracellular RNA in bodily fluid from a subject is contained within microvesicles and thus protected from degradation by ribonucleases (Skog et al., 2008). More than 90% of extracellular RNA in total serum can be recovered in microvesicles (Skog et al., 2008).
  • One aspect of the present invention relates to methods for detecting, diagnosing, monitoring, treating or evaluating a disease or other medical condition in a subject comprising the steps of, isolating exosomes from a bodily fluid of a subject, and analyzing one or more nucleic acids contained within the exosomes.
  • the nucleic acids are analyzed qualitatively and/or quantitatively, and the results are compared to results expected or obtained for one or more other subjects who have or do not have the disease or other medical condition.
  • the presence of a difference in microvesicular nucleic acid content of the subject, as compared to that of one or more other individuals, can indicate the presence or absence of, the progression of (e.g., changes of tumor size and tumor malignancy), or the susceptibility to a disease or other medical condition in the subject.
  • the isolation methods and techniques described herein provide the following heretofore unrealized advantages: 1) the opportunity to selectively analyze disease- or tumor- specific nucleic acids, which may be realized by isolating disease- or tumor- specific microvesicles apart from other microvesicles within the fluid sample; 2) significantly higher yield of nucleic acid species with higher sequence integrity as compared to the yield/integrity obtained by extracting nucleic acids directly from the fluid sample; 3) scalability, e.g.
  • the sensitivity can be increased by isolating more microvesicles from a larger volume of serum; 4) purer nucleic acids in that protein and lipids, debris from dead cells, and other potential contaminants and PCR inhibitors are excluded from the microvesicle preparation before the nucleic acid extraction step; and 5) more choices in nucleic acid extraction methods as microvesicle preparations are of much smaller volume than that of the starting serum, making it possible to extract nucleic acids from the microvesicle preparations using small volume column filters.
  • microvesicles are preferably isolated from a bodily fluid from a subject.
  • a "bodily fluid” refers to a sample of fluid isolated from anywhere in the body of the subject, preferably a peripheral location, including but not limited to, for example, blood, plasma, serum, urine, sputum, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, fluid of the respiratory, intestinal, and genitourinary tracts, tear fluid, saliva, breast milk, fluid from the lymphatic system, semen, cerebrospinal fluid, intra-organ system fluid, ascitic fluid, tumor cyst fluid, amniotic fluid and combinations thereof.
  • subject is intended to include all animals shown to or expected to have microvesicles.
  • the subject is a mammal, a human or nonhuman primate, a dog, a cat, a horse, a cow, other farm animals, or a rodent (e.g. mice, rats, guinea pig etc.).
  • rodent e.g. mice, rats, guinea pig etc.
  • subject and individual are used interchangeably herein.
  • Methods of isolating microvesicles from a biological sample are known in the art. For example, a method of differential centrifugation is described in a paper by Raposo et al. (Raposo et al., 1996) and a paper by Skog et. al.(Skog et al., 2008). Methods of anion exchange and/or gel permeation chromatography are described in US Patent Nos. 6,899,863 and 6,812,023. Methods of sucrose density gradients or organelle electrophoresis are described in U.S. Patent No. 7,198,923. A method of magnetic activated cell sorting
  • microvesicles can be identified and isolated from bodily fluid of a subject by a recently developed microchip technology that uses a microfluidic platform to separate tumor-derived microvesicles. This technology, as described in a paper by Nagrath et al. (Nagrath et al., 2007), can be adapted to identify and separate microvesicles using similar principles of capture and separation as taught in the paper. Further, a method of isolating microvesicles from urine samples is described in a paper by Miranda et.
  • the microvesicles isolated from a bodily fluid are enriched for those originating from a specific cell type, for example, lung, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colorectal, breast, prostate, brain, esophagus, liver, placenta, fetus cells.
  • a specific cell type for example, lung, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colorectal, breast, prostate, brain, esophagus, liver, placenta, fetus cells.
  • surface molecules may be used to identify, isolate and/or enrich for microvesicles from a specific donor cell type (Al-Nedawi et al., 2008; Taylor and Gercel-Taylor, 2008).
  • microvesicles originating from distinct cell populations can be analyzed for their nucleic acid content.
  • tumor (malignant and non- malignant) microvesicles carry tumor-associated surface antigens and may be detected, isolated and/or enriched via these specific tumor-associated surface antigens.
  • the surface antigen is epithelial-cell-adhesion-molecule (EpCAM), which is specific to microvesicles from carcinomas of lung, colorectal, breast, prostate, head and neck, and hepatic origin, but not of hematological cell origin (Balzar et al., 1999; Went et al., 2004).
  • the surface antigen is CD24, which is a glycoprotein specific to urine microvesicles (Keller et al., 2007).
  • the surface antigen is selected from a group of molecules including CD70, carcinoembryonic antigen (CEA), EGFR, EGFRvIII and other variants, Fas ligand, TRAIL, tranferrin receptor, p38.5, p97 and HSP72.
  • tumor- specific microvesicles may be characterized by the lack of surface markers, such as CD80 and CD86.
  • the isolation of microvesicles from specific cell types can be accomplished, for example, by using antibodies, aptamers, aptamer analogs or molecularly imprinted polymers specific for a desired surface antigen.
  • the surface antigen is specific for a cancer type.
  • the surface antigen is specific for a cell type which is not necessarily cancerous.
  • U.S. Patent No. 7,198,923. As described in, e.g., U.S. Patent Nos. 5,840,867 and 5,582,981, WO/2003/050290 and a publication by Johnson et al.
  • aptamers and their analogs specifically bind surface molecules and can be used as a separation tool for retrieving cell type- specific microvesicles.
  • Molecularly imprinted polymers also specifically recognize surface molecules as described in, e.g., US Patent Nos. 6,525,154, 7,332,553 and 7,384,589 and a publication by Bossi et al. (Bossi et al., 2007) and are a tool for retrieving and isolating cell type-specific microvesicles.
  • Bossi et al. Bossi et al.
  • nucleic acid molecules can be extracted from a microvesicle using any number of procedures, which are well-known in the art, the particular extraction procedure chosen being appropriate for the particular biological sample. In some instances, with some techniques, it may also be possible to analyze the nucleic acid without extraction from the microvesicle.
  • the extracted nucleic acids are analyzed directly without an amplification step.
  • Direct analysis may be performed with different methods including, but not limited to, nanostring technology.
  • NanoString technology enables identification and quantification of individual target molecules in a biological sample by attaching a color-coded fluorescent reporter to each target molecule. This approach is similar to the concept of measuring inventory by scanning barcodes.
  • Reporters can be made with hundreds or even thousands of different codes allowing for highly multiplexed analysis.
  • the technology is described in a publication by Geiss et al. (Geiss et al., 2008) and is incorporated herein by reference for this teaching.
  • nucleic acid of the microvesicle it may be beneficial or otherwise desirable to amplify the nucleic acid of the microvesicle prior to analyzing it.
  • Methods of nucleic acid amplification are commonly used and generally known in the art, many examples of which are described herein. If desired, the amplification can be performed such that it is quantitative. Quantitative amplification will allow quantitative determination of relative amounts of the various nucleic acids, to generate a profile as described below.
  • the extracted nucleic acid is RNA.
  • the RNA is reverse-transcribed into complementary DNA before further amplification.
  • Such reverse transcription may be performed alone or in combination with an amplification step.
  • a method combining reverse transcription and amplification steps is reverse transcription polymerase chain reaction (RT-PCR), which may be further modified to be quantitative, e.g., quantitative RT-PCR as described in US Patent No. 5,639,606, which is incorporated herein by reference for this teaching.
  • RT-PCR reverse transcription polymerase chain reaction
  • Nucleic acid amplification methods include, without limitation, polymerase chain reaction (PCR) (US Patent No. 5,219,727) and its variants such as in situ polymerase chain reaction (US Patent No. 5,538,871), quantitative polymerase chain reaction (US Patent No. 5,219,727), nested polymerase chain reaction (US Patent No.
  • nucleic acids present in the microvesicles are quantitative and/or qualitative.
  • amounts e.g., expression levels
  • expression levels either relative or absolute
  • all or specific species of nucleic acids of interest within the microvesicles, whether wild-type or variants, are identified with methods known in the art (described below).
  • a “profile” is used herein to refer to the result of a quantitative analysis, a qualitative analysis, or a combination of both.
  • the analysis may be an analysis of the nucleic acids as well as other contents extracted from a biological sample, e.g., a microvesicle.
  • a profile of genes refers to one or more genetic aberrations of the genes.
  • a “genetic aberration” is used herein to refer to a nucleic acid amount as well as a nucleic acid variant within a biological sample, e.g., a microvesicle.
  • genetic aberrations include, without limitation, over-expression of a gene (e.g., oncogenes) or a panel of genes, under-expression of a gene (e.g., tumor suppressor genes such as p53 or RB) or a panel of genes, alternative production of splice variants of a gene or a panel of genes, gene copy number variants (CNV) (e.g.
  • CNV gene copy number variants
  • DNA double minutes DNA double minutes
  • nucleic acid modifications e.g., methylation, acetylation and phosphorylations
  • single nucleotide polymorphisms SNPs
  • chromosomal rearrangements e.g., inversions, deletions and duplications
  • mutations insertions, deletions, duplications, missense, nonsense, synonymous or any other nucleotide changes
  • nucleic acid modifications can be assayed by methods described in, e.g., US Patent No. 7,186,512 and patent publication WO
  • methylation profiles may be determined by Illumina DNA Methylation OMA003 Cancer Panel.
  • SNPs and mutations can be detected by hybridization with allele- specific probes, enzymatic mutation detection, chemical cleavage of mismatched heteroduplex (Cotton et al., 1988), ribonuclease cleavage of mismatched bases (Myers et al., 1985), mass spectrometry (US Patent Nos.
  • nucleic acid sequencing single strand conformation polymorphism (SSCP) (Orita et al., 1989), denaturing gradient gel electrophoresis (DGGE)(Fischer and Lerman, 1979a; Fischer and Lerman, 1979b), temperature gradient gel electrophoresis (TGGE) (Fischer and Lerman, 1979a;
  • SSCP single strand conformation polymorphism
  • DGGE denaturing gradient gel electrophoresis
  • TGGE temperature gradient gel electrophoresis
  • gene expression levels may be determined by the serial analysis of gene expression (SAGE) technique (Velculescu et al., 1995).
  • the analysis is of a profile of the amounts (levels) of all or specific nucleic acids present in the microvesicle, herein referred to as a "quantitative nucleic acid profile" of the micro vesicles.
  • the analysis is of a profile of the species of all or specific nucleic acids present in the microvesicles (both wild type as well as variants), herein referred to as a "nucleic acid species profile.”
  • a term used herein to refer to a combination of these types of profiles is "genetic profile" which refers to the determination of the presence or absence of nucleotide species, variants and also increases or decreases in nucleic acid levels.
  • a profile can be a genome-wide profile (representing all possible expressed genes or DNA sequences). It can be narrower as well, such as a cancer-wide profile (representing all possible genes or nucleic acids derived from or associated with cancer). Where a specific cancer is suspected or known to exist, the profile can be specific to that cancer (e.g., representing all possible genes or nucleic acids derived from or associated with the cancer or various clinically distinct subtypes of that cancer or known drug -resistant or sensitive forms of the cancer).
  • microvesicles Many methods of diagnosis performed on a tumor biopsy sample can be performed with microvesicles since tumor cells are known to shed microvesicles into bodily fluid and the genetic aberrations within these microvesicles are reflective of those within the tumor cells themselves (Skog et al., 2008). Furthermore, methods of diagnosis using microvesicles have characteristics that are absent in methods of diagnosis performed directly on a tumor biopsy sample. For example, one particular advantage of the analysis of microvesicular nucleic acids, as opposed to other forms of sampling of tumor/cancer nucleic acid, is the availability for analysis of tumor/cancer nucleic acids derived from all foci of a tumor or genetically heterogeneous tumors present in an individual.
  • Biopsy samples are limited in that they provide information only about the specific focus of the tumor from which the biopsy is obtained. Different tumorous/cancerous foci found within the body, or even within a single tumor often have different genetic profiles, all of which are not analyzed in a standard biopsy. However, analysis of the microvesicular nucleic acids from an individual has the potential to provide a sampling of all foci within an individual. This provides valuable information with respect to recommended treatments, treatment
  • aspects of the present invention relate to a method for monitoring disease (e.g. cancer) progression in a subject, and also to a method for monitoring disease recurrence in an individual.
  • These methods comprise the steps of isolating microvesicles from a bodily fluid of an individual, as discussed herein, and analyzing nucleic acid within the microvesicles as discussed herein (e.g. to create a genetic profile of the microvesicles).
  • the presence or absence of a certain genetic aberration or profile is used to indicate the presence or absence of the disease (e.g., cancer) in the subject as discussed herein.
  • the process is performed periodically over time, and the results reviewed, to monitor the progression or regression of the disease, or to determine recurrence of the disease.
  • a change in the microvesicular genetic profile indicates a change in the disease state in the subject.
  • the period of time to elapse between sampling of microvesicles from the subject, for performance of the isolation and analysis of the microvesicles, will depend upon the circumstances of the subject, and is to be determined by the skilled practitioner.
  • Such a method would be extremely beneficial when analyzing nucleic acid from a gene that is associated with the therapy undergone by the subject.
  • a gene which is targeted by the therapy can be monitored for the development of mutations which make it resistant to the therapy, upon which time the therapy can be modified accordingly.
  • the monitored gene may also be one which indicates specific responsiveness to a specific therapy.
  • aspects of the present invention also relate to the fact that a variety of non- cancer diseases and/or medical conditions also have genetic links and/or causes, and such diseases and/or medical conditions can likewise be diagnosed and/or monitored by the methods described herein.
  • Many such diseases are metabolic, infectious or degenerative in nature.
  • diabetes e.g. diabetes insipidus
  • V2R vasopressin type 2 receptor
  • kidney fibrosis in which genetic profiles for the genes of collagens, fibronectin and TGF- ⁇ are changed. Changes in genetic profiles due to substance abuse, viral and/or bacterial infection, and hereditary disease states can likewise be detected by the methods described herein.
  • Diseases or other medical conditions for which the inventions described herein are applicable include, but are not limited to, nephropathy, diabetes insipidus, diabetes mellitus, diabetes type I, diabetes II, renal disease glomerulonephritis, bacterial or viral glomerulonephritides, IgA nephropathy, Henoch-Schonlein Purpura, membranoproliferative glomerulonephritis, membranous nephropathy, Sjogren's syndrome, nephrotic syndrome minimal change disease, focal glomerulosclerosis and related disorders, acute renal failure, acute tubulointerstitial nephritis, pyelonephritis, GU tract inflammatory disease, Pre- clampsia, renal graft rejection, leprosy, reflux nephropathy, nephrolithiasis, genetic renal disease, medullary cystic, medullar sponge, polycystic kidney disease, autosomal dominant poly
  • erythematosus gout, blood disorders, sickle cell disease, thrombotic thrombocytopenia purpura, Fanconi's syndrome, transplantation, acute kidney injury, irritable bowel syndrome, hemolytic-uremic syndrome, acute corticol necrosis, renal thromboembolism, trauma and surgery, extensive injury, burns, abdominal and vascular surgery, induction of anesthesia, side effect of use of drugs or drug abuse, circulatory disease myocardial infarction, cardiac failure, peripheral vascular disease, hypertension, coronary heart disease, non-atherosclerotic cardiovascular disease, atherosclerotic cardiovascular disease, skin disease, psoriasis, systemic sclerosis, respiratory disease, COPD, obstructive sleep apnoea, hypoia at high altitude or endocrine disease, or acromegaly.
  • the cancer diagnosed, monitored or otherwise profiled can be any kind of cancer. This includes, without limitation, epithelial cell cancers such as lung, ovarian, cervical, endometrial, breast, brain, colon and prostate cancers. Also included are
  • gastrointestinal cancer, head and neck cancer non- small cell lung cancer, cancer of the nervous system, kidney cancer, retina cancer, skin cancer, liver cancer, pancreatic cancer, genital-urinary cancer and bladder cancer, melanoma, and leukemia.
  • the methods and compositions of the present invention are equally applicable to detection, diagnosis and prognosis of non-malignant tumors in an individual (e.g., neurofibromas, meningiomas and schwannomas).
  • the cancer is brain cancer.
  • Types of brain tumors and cancer are well known in the art.
  • Glioma is a general name for tumors that arise from the glial (supportive) tissue of the brain.
  • Gliomas are the most common primary brain tumors.
  • Astrocytomas, ependymomas, oligodendrogliomas, and tumors with mixtures of two or more cell types, called mixed gliomas, are the most common gliomas.
  • Neurinoma Adenoma
  • Adenoma Adenoma
  • Astracytoma Low-Grade Astrocytoma
  • giant cell astrocytomas Mid- and High-Grade Astrocytoma
  • Recurrent tumors Brain Stem Glioma, Chordoma, Choroid Plexus Papilloma, CNS Lymphoma (Primary Malignant Lymphoma), Cysts, Dermoid cysts, Epidermoid cysts, Craniopharyngioma, Ependymoma Anaplastic ependymoma,
  • Gangliocytoma (Ganglioneuroma), Ganglioglioma, Glioblastoma Multiforme (GBM), Malignant Astracytoma, Glioma, Hemangioblastoma, Inoperable Brain Tumors, Lymphoma, Medulloblastoma (MDL), Meningioma, Metastatic Brain Tumors, Mixed Glioma,
  • Neurofibromatosis Oligodendroglioma. Optic Nerve Glioma, Pineal Region Tumors, Pituitary Adenoma, PNET (Primitive Neuroectodermal Tumor), Spinal Tumors,
  • one aspect of the present invention is a method of analyzing RNA profiles using microvesicles isolated from brain cancer serum samples.
  • the method comprises the steps of isolating microvesicles from brain cancer serum samples and analyzing nucleic acids extracted from the isolated microvesicles.
  • Another aspect of the present intention is the discovery of a series of brain cancer gene expression profiles or signatures.
  • the signatures were discovered by analyzing nucleic acids extracted from brain cancer serum samples.
  • the signatures can be used for the diagnosis and /or prognosis of brain caner, as well as treatment plan evaluation, selection and monitoring of brain cancer.
  • Vacutainer SST (#367985) at Massachusetts General Hospital (MGH). Blood from normal healthy controls was collected from volunteers recruited at the MGH blood bank. All samples were collected with informed consent according to the appropriate protocols approved by the Institutional Review Board at MGH. The blood was left to clot for 30 min and serum was isolated according to manufacturer's recommendations within two hours of collection. Serum was filtered by slowly passing it through a 0.8 ⁇ syringe filter, aliquoted into 1.8 milliliter (ml) cryotubes and kept at -80°C until used. Altogether, 9 serum samples from glioblastoma patients and 7 serum samples from non-glioblastoma human subjects were obtained for the following analysis.
  • microvesicle pellets were washed in 13 ml PBS, pelleted again and resuspended in cold PBS. Isolated microvesicles were measured for their total protein content using DC Protein Assay (Bio-Rad, Hercules, CA, USA).
  • RNAse inhibitor solution for 5-10 minutes at room temperature.
  • the RNase inhibitor can be from various known vendors, e.g., one inhibitor is "SUPERase" from
  • Genome Oligo Microarrays (one-color), a standard gene expression analysis tool, according to standard protocols. Briefly, for the linear T7-based amplification step, from 0.07 ⁇ g up to 0.46 (.ig of total RNA was used, depending on the available amount of total RNA. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).
  • the hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.5 -1.65 ⁇ g of Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile. Fluorescence signals of the hybridized Agilent
  • Microarrays were detected using Agilent's Microarray Scanner System (Agilent
  • FES Agilent Feature Extraction Software
  • the raw data from Feature Extraction was pre-processed and normalized in several different ways using R/Bioconductor and the packages limma, Agi4x44PrePro ess and vsn. To ensure that the normalization procedure did not introduce unintended biases or artifacts, the data was normalized in three different ways using Quartile normalization with and without background subtraction and variance stabilized normalization (VSN), and the normalized data was compared to the raw values. Normalized data was transferred to Excel and filtered with different criteria as described below. Gene lists of interest were uploaded and analyzed with the online Gene Ontology Tool DAVID 6.7
  • RNA from this exosomal fraction was extracted, labeled and amplified by linear amplification and hybridized to Agilent 4x44K arrays.
  • the raw data was corrected for background, normalized and submitted for deposit in the Gene Expression Omnibus database by user name/ID Mikkell Noerholm on September 4, 2010 in the format of GEOarchive.
  • the deposited file name is AgilentQuartileNorm_MeanSignal_GBMvsCTRL_GEO.zip.
  • the deposited data are here incorporated by reference in its entirety including the array oligo sequences.
  • Clustering analysis, heat maps, and Principle Component Analysis of the normalized data was performed by using various softwares, e.g. GeneSifter, provided various sources, e.g., dChip (http://biosunl.harvard.edu/complab/dchip).
  • GeneSifter provided various sources, e.g., dChip (http://biosunl.harvard.edu/complab/dchip).
  • a clustering analysis for genome-wide expression data from DNA microarray hybridization uses standard statistical algorithms to cluster genes according to similarity in pattern of gene expression (Eisen et al., 1998).
  • a type of Principle Component Analysis is described previously (Alter et al., 2000).
  • Table 1 p ⁇ 5xl0 ⁇ 4 and with the log-median-ratio being at least "1" or above, or p ⁇ 0.000002;
  • Table 6 p ⁇ 5xl0 "4 and the log-median-ratio being at least "0.8” or above, or being at least "-0.8” or below;
  • Table 7 p ⁇ lxlO "5 and the log-median-ratio being at least "0.585” or above, or being at least "-0.585” or below;
  • Table 8 p ⁇ lxlO "4 and the log-median-ratio being at least "1" or above, or being at least or below;
  • Table 12 p ⁇ lxlO "3 and the log-median-ratio being at least "1" or above, or being or below;
  • Table 13 p ⁇ 0.05 and the log-median-ratio being at least "1" or above, or being or below;
  • Each of the 16 groups can be a gene signature for glioblastoma.
  • two independent tests were performed.
  • One test used Clustering Analysis.
  • the other test used Principle Component Analysis.
  • the results showed that at least one of the two tests separated the cancer group and the control group.
  • one embodiment of the present invention is a profile of one or more of genes selected from the genes in Tables 1-16.
  • the profiles are of one or more genes selected from a single Table, e.g., from Table 1.
  • the profiles are of a group of genes comprising each of the genes in a single Table, e.g., Tablel.
  • One or more members in each group constitute a glioblastoma gene signature because either Clustering Analysis or Principle Component Analysis of the expression profiles of such one or more members in each group can separate the disease and control samples.
  • Another embodiment of the present invention is a method of applying the signatures for aiding the diagnosis, prognosis or therapy treatment for a subject.
  • the method comprises first isolating microvesicles from the subject, measuring the expression levels of one or more RNA transcripts extracted from isolated microvesicles, determining a test profile of one or more RNA transcripts based on the measured expression level(s), and comparing the test profile to a reference profile to determine the characteristics of the test profile.
  • the group included 22 genes based on the inclusion criteria of p ⁇ 5xl0 ⁇ 4 and a log-median-ratio being at least "1" or above, or p ⁇ 0.000002.
  • the 22 genes have functionalities including as receptors, transcription factors, and enzymes.
  • the 22-gene signature clusters control samples together in one subgroup and disease samples together in another subgroup when subjected to a Clustering Analysis.
  • the disease samples GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20 cluster together in one subgroup.
  • control samples from non-Glioblastoma human subjects Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8, clustered in another subgroup.
  • the separation of GBM and Control samples can be achieved by Clustering Analysis.
  • Figure IB the same 22-gene signature is validated using Principle Component Analysis.
  • the Control group dots appear on the upper left side of the plot while the GBM group dots appear on the middle-right side of the plot.
  • an evidence-based analysis tool may also be used for analyzing expression data.
  • a gene ontology analysis may be carried out and genes in the same biological signaling pathway group together.
  • a signature or profile comprised of a group of genes in a relevant signaling pathway may be derived and used for the purpose of diagnosing a corresponding biological condition.
  • ribonucleoprotein Furthermore, 24 genes were found to be upregulated. Using the above- mentioned criteria, a GO analysis with an enrichment score of 1.27 showed that 23 recognized genes had GO terms related to transcription (i.e. transcription factor activity, transcription, DNA binding, homeobox).
  • Table 17 p ⁇ 5xl0 ⁇ 2 and with the log-median-ratio being at least "1" or above, or being at least or below;
  • Table 18 p ⁇ 5xl0 ⁇ 2 and the log-median-ratio being at least "1" or above, or being at least "- 1.5" or below;
  • Table 19 p ⁇ 5xl0 ⁇ 2 and the log-median-ratio being at least "1" or above;
  • Each of the 4 groups can be a gene signature for glioblastoma. We tested each group for its capability as a glioblastoma signature. For each group, two independent tests were performed. One test used Clustering Analysis. The other test used Principle
  • the group includes 31 genes based in the inclusion criteria of p ⁇ 5xl0 ⁇ and the log- median-ratio being at least "1" or above, or being at least "-1.5” or below.
  • the 31 genes have various functionalities including as receptors, transcription factors, and enzymes.
  • the 31 -gene signature clusters control samples together in one subgroup and disease samples together in another subgroup when subjected to Clustering Analysis.
  • the 9 tumor samples are easily distinguishable from and clearly form a cluster different from the 7 Normal Controls.
  • the disease samples GBM11, GBM12, GBM13, GBM15, GBM16, GBM 17, GBM18, GBM19, and GBM20 cluster together in one subgroup.
  • control samples from non-Glioblastoma human subjects Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8, clustered in another subgroup.
  • the separation of GBM and Control samples can be achieved by Clustering Analysis.
  • Figure 19B the same 31 -genes signature was validated using Principle Component Analysis.
  • the Control group dots appear on the upper left side of the plot.
  • the GBM group dots appear on the middle-right side of the plot.
  • Gap-LCR modified ligase chain reaction
  • Kan, Y.W., and A.M. Dozy. 1978a Antenatal diagnosis of sickle-cell anaemia by D.N.A. analysis of amniotic-fluid cells. Lancet. 2:910-2.
  • CD24 is a marker of exosomes secreted into urine and amniotic fluid. Kidney Int. 72: 1095-102.
  • UV and skin cancer specific p53 gene mutation in normal skin as a biologically relevant exposure measurement. Proc Natl Acad Sci U S A. 91:360-4.
  • RNA. 13:1027-35 Human cell growth requires a functional cytoplasmic exosome, which is involved in various mRNA decay pathways. RNA. 13:1027-35.

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Abstract

The invention concerns gene signatures obtained from microvesicles and a method of applying these gene signatures in helping to determine a biological condition. The determination of a biological condition may aid, for example, the diagnosis, prognosis, and therapy treatment selection for a disease in a subject.

Description

USE OF MICRO VESICLES IN ANALYZING NUCLEIC ACID PROFILES
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This Application claims the benefit of priority under 35 U.S.C. § 119(e) of US
Provisional Application Serial Number 61/241,014 filed September 9, 2009, the contents of which are incorporated herein by reference in their entirety.
FIELD OF INVENTION
[0002] The present invention relates to the general fields of nucleic acid analysis in human or other animal subjects, particularly the profiling of nucleic acids from a biological sample, and in particular, from micro vesicles.
BACKGROUND
[0003] Cancer molecular diagnostics is becoming increasingly important with the accumulating knowledge of the molecular mechanisms underlying various types of cancers and the implications for diagnosis, treatment selection and prognosis.
[0004] Various molecular diagnostic tests like mutational analysis, methylation status of genomic DNA and gene expression analysis are currently being used to answer clinical questions. Differential gene expression analysis of cancer cells has so far primarily been done on cancer cells derived from surgically removed tumor tissue or from tissue obtained by biopsy. However, the ability to profile gene expression using a blood sample from a cancer patient rather than a tissue sample is desirable because a non-invasive approach such as this has wide ranging implications in terms of patient welfare, the ability to conduct longitudinal disease monitoring, and the ability to obtain expression profiles even when tissue cells are not easily accessible, e.g., in ovarian or brain cancer patients.
[0005] So far, gene expression profiling using a blood sample is confined to analyzing RNA extracted from Peripheral Blood Mononuclear Cells (PBMC) (Hakonarson et al., 2005) or Circulating Tumor Cells (CTC) (Cristofanilli and Mendelsohn, 2006). This invention discloses a novel method of profiling gene expressions and provides novel gene expression signatures associated with diseases by analyzing nucleic acids extracted from microvesicles from a bodily fluid, e.g., a blood sample.
BRIEF SUMMARY OF THE INVENTION
[0006] The present invention provides genetic profiles associated with biological conditions and methods of applying these profiles in evaluating the biological conditions. As such, in one aspect, the present invention is directed to a profile of one or more RNA transcripts obtained from microvesicles. The one or more RNA transcripts are selected from those listed in Tables 1-20. In one embodiment, the microvesicles from which the profile is obtained are isolated from a bodily fluid from a subject. The bodily fluid may be blood, serum, plasma or urine. In a further embodiment, the subject is a human subject. In an even further embodiment, the human subject is a brain cancer patient such as a glioblastoma patient.
[0007] In another embodiment, the profile is obtained through analyzing RNA transcripts obtained from microvesicles. The analysis of RNA transcripts is performed by a method such as microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination of these above methods. In a further embodiment, the analysis includes an additional step of data analysis. The data analysis can be accomplished with Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis, Binary Analysis, Cox Proportional Hazards Analysis, Support Vector Machines and Recursive Feature Elimination (SVM-RFE), Classification to Nearest Centroid, Evidence-based Analysis, or a combination of the above methods. In yet another embodiment, the profile obtained from microvesicles is a profile of the one or more RNA transcripts selected from any one of the Tables 1-20. In yet another embodiment, the profile from microvesicles is a profile of each of the RNA transcripts listed in any one of the Tables 1-20.
[0008] In another aspect, the present invention refers to a method of aiding diagnosis, prognosis or therapy treatment planning for a subject, comprising the steps of: a) isolating microvesicles from a subject; b) measuring the expression level of one or more RNA transcripts extracted from the isolated microvesicles; c) determining a profile of the one or more RNA transcripts based on the expression level; and d) comparing the profile to a reference profile to aid diagnosis, prognosis or therapy treatment planning for the subject. In one embodiment, the microvesicles used in the method are isolated from a bodily fluid from the subject. The bodily fluid may be blood, serum, plasma or urine. In a further embodiment, the subject is a human subject. In an even further embodiment, the human subject is a brain cancer patient such as a glioblastoma patient. The step (b) in the method is accomplished with a microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination of the above methods. In a further embodiment, the step (c) in the method includes an additional step of data analysis. The data analysis can be accomplished with Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis, Binary Analysis, Cox Proportional Hazards Analysis, Support Vector Machines and Recursive Feature Elimination (SVM-RFE), Classification to Nearest Centroid, Evidence-based Analysis, or a combination of the above methods. The RNA transcripts whose profiles are determined in are one or more RNA transcripts selected from those listed in Tables 1-20. In yet another embodiment, the RNA transcripts whose profiles are determined include one or more RNA transcripts selected from any one of the Tables 1- 20. In a further embodiment, the RNA transcripts are all of the transcripts listed in any one of Tables 1-20.
[0009] In yet another aspect, the present invention refers to a method of preparing a personalized genetic profile report for a subject, comprising the steps of: (a) isolating microvesicles from a subject; (b) detecting or measuring one or more genetic aberrations within the isolated microvesicles; (c) determining one or more genetic profiles from the data obtained from steps (a) and (b); (d) optionally comparing the one or more genetic profiles to one or more reference profiles; and (e) creating a report summarizing the data obtained from steps (a) through (d) and optionally including diagnostic, prognostic or therapeutic treatment information. In one embodiment of the method, step (b) comprises the quantitative measurement of one or more nucleic acids within the isolated microvesicles and step (c) comprises the determination of one or more quantitative nucleic acid profiles. In another embodiment of the method, the one or more nucleic acids are RNA transcripts selected from Tables 1-20. In a further embodiment of the method, the one or more nucleic acids are RNA transcripts selected from any one of Tables 1- 20. In another further embodiment of the method, one or more nucleic acids comprise each of the RNA transcripts in any one of the Tables 1-20.
[0010] In yet another aspect, the present invention is a kit for genetic analysis of an exosome preparation from a body fluid sample from a subject, comprising, in a suitable container, one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from Tables 1-20. In one embodiment, the kit includes one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from any one of Tables 1-20. In another embodiment, the kit includes one or more reagents suitable for hybridizing to or amplifying each of the RNA transcripts in any one of Tables 1- 20. [0011] In yet another aspect, the present invention is a custom-designed oligonucleotide microarray for genetic analysis of an exosome preparation from a body fluid sample from a subject, wherein the oligos on the array exclusively hybridize to one or more transcripts selected from any one of Tables 1-20.
[0012] In yet another aspect, the present invention is a method of identifying at least one potential biomarker for a disease or other medical condition, the method comprising: (a) isolating microvesicles from subjects having a disease or other medical condition of interest and from subjects who do not have the disease or other medical condition of interest; (b) measuring the expression level of a target RNA transcript extracted from the isolated microvesicles from each of the subjects; (c) comparing the measured levels of the target RNA transcript from each of the subjects; and (d) determining whether there is a statistically significant difference in the measured levels; wherein a determination resulting from step (d) of a statistically significant difference in the measured levels identifies the target RNA transcript and its corresponding gene as potential biomarkers for the disease or other medical condition. Preferably, the target RNA transcript is selected from Tables 1-20.
[0013] In yet another aspect, the present invention is a method of profiling genetic aberrations in a subject, comprising the steps of: (a) isolating microvesicles from a subject; (b) detecting or measuring one or more genetic aberrations within the isolated microvesicles; and (c) determining one or more genetic profiles from the data obtained from steps (a) and (b). In one embodiment of the method, step (b) comprises the quantitative measurement of one or more nucleic acids within the isolated microvesicles and step (c) comprises the determination of one or more quantitative nucleic acid profiles. In a further embodiment of the method, the one or more nucleic acids are RNA transcripts selected from Tables 1-20. In another embodiment, the one or more nucleic acids are RNA transcripts selected from any one of Tables 1- 20. In yet another further embodiment, the one or more nucleic acids comprise each of the RNA transcripts in any one of Tables 1-20. In any of the inventive methods, a step of enriching the isolated microvesicles for microvesicles originating from a specific cell type may be optionally included.
[0014] The present invention may be as defined in any one of the following numbered paragraphs.
1. A profile of one or more RNA transcripts obtained from microvesicles, wherein the one or more RNA transcripts are selected from Tables 1-20.
2. The profile of paragraph 1, wherein the microvesicles are isolated from a bodily fluid from a subject.
3. The profile of paragraph 2, wherein the bodily fluid is blood, serum, plasma or urine.
4. The profile of paragraph 2, wherein the subject is a human subject.
5. The profile of paragraph 4, wherein the human subject is a brain cancer patient.
6. The profile of paragraph 5, wherein the brain cancer is glioblastoma.
7. The profile of paragraph 1, wherein the profile is obtained through analyzing RNA transcripts obtained from microvesicles.
8. The profile of paragraph 7, wherein the analysis of RNA transcripts is performed by a method comprising microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination thereof.
9. The profile of paragraph 8, wherein the analytic method further comprises data
analysis.
10. The profile of paragraph 9, wherein the data analysis comprises Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis, Binary Analysis, Cox Proportional Hazards Analysis, Support Vector Machines and Recursive Feature Elimination (SVM-RFE), Classification to Nearest Centroid, Evidence-based Analysis, or a combination thereof. The profile of paragraph 10, wherein the data analysis comprises Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, or a combination thereof. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 1. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 1. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 2. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 2. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 3. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 3. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 4. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 4. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 5. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 5. The profile paragraph 1, wherein the one or more RNA transcripts are selected from Table 6. The profile of paragraph 1, wherein the one or more RNAs transcripts comprise each of the transcripts in Table 6. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 7. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 7. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 8. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 8. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 9. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 9. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 10. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 10. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 11. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 11. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 12. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 12. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 13.
The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 13.
The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 14.
The profile of paragraph 1, wherein the one or more RNA transcript comprise each of the transcripts in Table 14.
The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 15.
The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 15.
The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 16.
The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 16.
The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 17.
The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 17.
The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 18.
The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 18.
The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 19. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 19. The profile of paragraph 1, wherein the one or more RNA transcripts are selected from Table 20. The profile of paragraph 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 20. A method of aiding diagnosis, prognosis or therapy treatment planning for a subject, comprising: a. isolating microvesicles from a subject; b. measuring the expression level of one or more RNA transcripts extracted from the isolated microvesicles; c. determining a profile of the one or more RNA transcripts based on the
expression level; and d. comparing the profile to a reference profile to aid diagnosis, prognosis or therapy treatment planning for the subject. The method of paragraph 52, wherein the microvesicles are isolated from a bodily fluid from the subject. The method of paragraph 53, wherein the bodily fluid is blood, plasma, serum or urine. The method of paragraph 53, wherein the subject is a human subject. The method of paragraph 55, wherein the human subject is a brain cancer patient. The method of paragraph 55, wherein the brain cancer is glioblastoma. The method of paragraph 52, wherein step (b) is performed by a method comprising microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination thereof. The method of paragraph 52, wherein step (c) performed by a method of data analysis. The method of paragraph 59, wherein the data analysis comprises Clustering
Analysis, Principle Component Analysis, Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis, Binary Analysis, Cox Proportional Hazards Analysis, Support Vector Machines and Recursive Feature Elimination (SVM-RFE), Classification to Nearest Centroid, Evidence-based Analysis, or a combination thereof. The method of paragraph 60, wherein the data analysis comprises Clustering
Analysis, Principle Component Analysis, Linear Discriminant Analysis, or a combination thereof. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Tables 1-16. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 1. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 1. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 2. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 2. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 3. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 3. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 4. 70. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 4.
71. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 5.
72. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 5.
73. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 6.
74. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 6.
75. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 7.
76. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 7.
77. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 8.
78. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 8.
79. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 9.
80. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 9.
81. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 10.
82. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 10. 83. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 11.
84. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 11.
85. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 12.
86. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 12.
87. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 13.
88. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 13.
89. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 14.
90. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 14.
91. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 15.
92. The method in paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 15.
93. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 16.
94. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 16.
95. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 17. 96. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 17.
97. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 18.
98. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 18.
99. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 19.
100. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 19.
101. The method of paragraph 52, wherein the one or more RNA transcripts are selected from Table 20.
102. The method of paragraph 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 20.
103. A method of preparing a personalized genetic profile report for a subject, comprising the steps of:
(a) isolating microvesicles from a subject;
(b) detecting or measuring one or more genetic aberrations within the isolated microvesicles;
(c) determining one or more genetic profiles from the data obtained from steps (a) and (b);
(d) optionally comparing the one or more genetic profiles to one or more
reference profiles; and
(e) creating a report summarizing the data obtained from steps (a) through (d) and optionally including diagnostic, prognostic or therapeutic treatment information. 104. The method of paragraph 103, wherein step (b) comprises the quantitative
measurement of one or more nucleic acids within the isolated microvesicles and step (c) comprises the determination of one or more quantitative nucleic acid profiles.
105. The method of paragraph 104, wherein the one or more nucleic acids are RNA
transcripts selected from Tables 1-20.
106. The method of paragraph 104, wherein the one or more nucleic acids are RNA
transcripts selected from any one of Tables 1- 20.
107. The method of paragraph 104, wherein the one or more nucleic acids comprise each of the RNA transcripts in any one of Tables 1-20.
108. A kit for genetic analysis of an exosome preparation from a body fluid sample from a subject, comprising, in a suitable container, one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from Tables 1-20.
109. The kit of paragraph 108, comprising one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from any one of Tables 1- 20.
110. The kit of paragraph 108, comprising one or more reagents suitable for hybridizing to or amplifying each of the RNA transcripts in any one of Tables 1-20.
111. An oligonucleotide microarray for genetic analysis of an exosome preparation from a body fluid sample from a subject, wherein the oligos on the array are custom-designed to hybridize exclusively to one or more transcripts selected from Tables 1-20.
112. A method of identifying at least one potential biomarker for a disease or other medical condition, the method comprising:
(a) isolating microvesicles from subjects having a disease or other medical
condition of interest and from subjects who do not have the disease or other medical condition of interest;
(b) measuring the expression level of a target RNA transcript extracted from the isolated microvesicles from each of the subjects; (c) comparing the measured levels of the target RNA transcript from each of the subjects; and
(d) determining whether there is a statistically significant difference in the
measured levels;
113. The method of paragraph 112, wherein a determination resulting from step (d) of a statistically significant difference in the measured levels identifies the target RNA transcript and its corresponding gene as potential biomarkers for the disease or other medical condition, and wherein the target RNA transcript is selected from Tables 1- 20.
114. A method of profiling genetic aberrations in a subject, comprising the steps of:
(a) isolating microvesicles from a subject;
(b) detecting or measuring one or more genetic aberrations within the isolated microvesicles;
(c) determining one or more genetic profiles from the data obtained from steps (a) and (b).
115. The method of paragraph 114, wherein step (b) comprises the quantitative
measurement of one or more nucleic acids within the isolated microvesicles and step (c) comprises the determination of one or more quantitative nucleic acid profiles.
116. The method of paragraph 114, wherein the one or more nucleic acids are RNA
transcripts selected from Tables 1-20.
117. The method of paragraph 114, wherein the one or more nucleic acids are RNA
transcripts selected from any one of Tables 1- 20.
118. The method of paragraph 114, wherein the one or more nucleic acids comprise each of the RNA transcripts in any one of Tables 1-20.
119. The method of any of paragraphs 52, 103, 112 or 114, further comprising the step of enriching the isolated microvesicles for microvesicles originating from a specific cell type. BRIEF DESCRIPTION OF THE DRAWINGS
[0015] FIGURE 1A. Heatmap and Clustering diagram illustrating microarray data showing gene expression profiles from exosomes isolated from serum samples from
Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM 19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 5xl0 and with the log-median-ratio (i.e. the logarithm to the ratio between the median expression level of a given gene in GBMs and the same gene in Ctrls,
log(median(GeneX(GBMs))/median(GeneX(Ctrls)))) being at least "1" or above, or with a P value less than or equal to 2xl0~6. The genes included in the data set are listed in Table 1.
[0016] FIGURE IB. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 1A with the same samples, the same genes and the same inclusion criteria.
[0017] FIGURE 2A. Heatmap and Clustering diagram illustrating microarray data showing gene expression profiles from exosomes isolated from serum samples from
Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM 19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 5xl0 and with the log-median-ratio being at least "1" or above. The genes included in the data set are listed in Table 2.
[0018] FIGURE 2B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 2A with the same samples, the same genes and the same inclusion criteria.
[0019] FIGURE 3A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM 13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 1x10° and with the log-median-ratio being at least "1" or above. The genes included in the data set are listed in Table 3.
[0020] FIGURE 3B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 3A with the same samples, the same genes and the same inclusion criteria.
[0021] FIGURE 4A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 2xl0~6. The genes included in the data set are listed in Table 4.
[0022] FIGURE 4B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 4A with the same samples, the same genes and the same inclusion criteria.
[0023] FIGURE 5A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO"5. The genes included in the data set are listed in Table 5.
[0024] FIGURE 5B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 5A with the same samples, the same genes and the same inclusion criteria.
[0025] FIGURE 6A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO"4 and with the log-median-ratio being at least "0.8" or above, or being at least "-0.8" or below. The genes included in the data set are listed in Table 6.
[0026] FIGURE 6B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 6A with the same samples, the same genes and the same inclusion criteria.
[0027] FIGURE 7A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO"5 and with the log-median-ratio being at least "0.585" or above, the log-median-ratio being at least "0.8" or above, or being at least "-0.585" or below. The genes included in the data set are listed in Table 7.
[0028] FIGURE 7B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 7A with the same samples, the same genes and the same inclusion criteria.
[0029] FIGURE 8A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO"4 and with the log-median-ratio being at least "1" or above, or being at least or below. The genes included in the data set are listed in Table 8.
[0030] FIGURE 8B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 8A with the same samples, the same genes and the same inclusion criteria.
[0031] FIGURE 9A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM 18, GBM 19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO"5 and with the log-median-ratio being below "0". The genes included in the data set are listed in Table 9.
[0032] FIGURE 9B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 9A with the same samples, the same genes and the same inclusion criteria.
[0033] FIGURE 10A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO 5 and with the log-median-ratio being above "0". The genes included in the data set are listed in Table 10.
[0034] FIGURE 10B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 10A with the same samples, the same genes and the same inclusion criteria.
[0035] FIGURE 11 A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM 19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, CtrB, Ctrl7 and Ctrl8. The heatmap shown is a part of the heatmap showing the expression of the genes listed in Table 11. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 1x104.
[0036] FIGURE 1 IB. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 11A with the same samples, the same genes and the same inclusion criteria.
[0037] FIGURE 12A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to lxlO 3 and with the log-median-ratio being at least "1" or above, or being or below. The genes included in the data set are listed in Table 12.
[0038] FIGURE 12B. A plot showing the result of a Principle Component Analysis
(PC A) performed on the data set of Figure 12A with the same samples, the same genes and the same inclusion criteria.
[0039] FIGURE 13 A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, CtrB, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 0.05 and with the log- median-ratio being at least "1" or above, or being or below. The genes included in the data set are listed in Table 13.
[0040] FIGURE 13B. A plot showing the result of a Principle Component Analysis
(PC A) performed on the data set of Figure 13A with the same samples, the same genes and the same inclusion criteria. [0041] FIGURE 14A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM 13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 0.05 and with the log- median-ratio being at least "0.585" or above. The genes included in the data set are listed in Table 14.
[0042] FIGURE 14B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 14A with the same samples, the same genes and the same inclusion criteria.
[0043] FIGURE 15 A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 0.05 and with the log- median-ratio being at least "1" or above. The genes included in the data set are listed in Table 15. [0044] FIGURE 15B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 15A with the same samples, the same genes and the same inclusion criteria.
[0045] FIGURE 16A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. The heatmap shown is a part of the heatmap showing the expression of the genes listed in Table 16. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a P value less than or equal to 0.001.
[0046] FIGURE 16B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 16A with the same samples, the same genes and the same inclusion criteria.
[0047] FIGURE 17. Volcano plot of -log(p- value) of the t-test between the two groups (GBM vs. Non-GBM) plotted against the differential expression of each gene between groups(M=log(GBM)-log(Ctrl), i.e. M=l means 2-fold up-regulation).
[0048] FIGURE 18 A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. The heatmap shown is a part of the heatmap showing the expression of the genes listed in Table 17. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a p<5xl0~2 and the log-median-ratio being at least "1" or above or being at least or below. The p-values were corrected using Benjamin and Hochberg method.
[0049] FIGURE 18B. A plot showing the result of a Principle Component Analysis
(PC A) performed on the data set of Figure 18A with the same samples, the same genes and the same inclusion criteria.
[0050] FIGURE 19A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. The heatmap shows the expression of the genes listed in Table 18. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are
significantly different with a p<5xl0~2 and the log-median-ratio being at least "1" or above or being at least "-1.5" or below. The p-values were corrected using Benjamin and Hochberg method.
[0051] FIGURE 19B. A plot showing the result of a Principle Component Analysis
(PC A) performed on the data set of Figure 19A with the same samples, the same genes and the same inclusion criteria.
[0052] FIGURE 20A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM12, GBM13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, Ctrl5, Ctrl7 and Ctrl8. The heatmap shows the expression of the genes listed in Table 19. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are
significantly different with a p<5xl0~2 and the log-median-ratio being at least "1" or above. The p-values were corrected using Benjamin and Hochberg method.
[0053] FIGURE 20B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 20A with the same samples, the same genes and the same inclusion criteria.
[0054] FIGURE 21A. Heatmap and Clustering diagram illustrating the microarray data showing gene expression profiles from exosomes isolated from serum samples from Glioblastoma (GBM) and non-Glioblastoma human subjects (Ctrl). The GBM RNA samples from glioblastoma patients are named GBM11, GBM 12, GBM 13, GBM15, GBM 16, GBM17, GBM18, GBM19, and GBM20. The control RNA samples from non-Glioblastoma human subjects are named Ctrll, Ctrl2, CtrB, Ctrl4, CtrB, Ctrl7 and Ctrl8. The heatmap shown is a part of the heatmap showing the expression of the genes listed in Table 20. For each of the genes included in the data set, the expression levels in the GBM samples and in the control samples are significantly different with a p<5xl0"2 and the log-median-ratio being at least "- 1.5" or below. The p-values were corrected using Benjamin and Hochberg method.
[0055] FIGURE 21 B. A plot showing the result of a Principle Component Analysis
(PCA) performed on the data set of Figure 21 A with the same samples, the same genes and the same inclusion criteria. DETAILED DESCRIPTION OF THE INVENTION
[0056] Microvesicles are shed by eukaryotic cells, or budded off of the plasma membrane, to the exterior of the cell. These membrane vesicles are heterogeneous in size with diameters ranging from about 10 nm to about 5000 nm. The small microvesicles (approximately 10 to 1000 nm, and more often approximately 30 to 200 nm in diameter) that are released by exocytosis of intracellular multivesicular bodies or by double inward budding of multivesicular bodies are referred to in the art as "exosomes." The compositions, methods and uses described herein are equally applicable to microvesicles of all sizes; preferably 30 to 800 nm; and more preferably 30 to 200 nm.
[0057] In some of the literature, the term "exosome" also refers to protein complexes containing exoribonucleases which are involved in mRNA degradation and the processing of small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNA) (Liu et al., 2006; van Dijk et al., 2007). Such protein complexes do not have membranes and are not "microvesicles" or "exosomes" as those terms are used here in.
[0058] Certain aspects of the present invention are based on the surprising finding that glioblastoma derived microvesicles can be isolated from the serum of glioblastoma patients (Skog et al., 2008). This is the first discovery of microvesicles derived from cells in the brain, present in a bodily fluid of a subject. Prior to this discovery it was not known whether glioblastoma cells produced microvesicles or whether such microvesicles could cross the blood brain barrier into the rest of the body. These microvesicles were found to contain mutant mRNA associated with tumor cells (Skog et al., 2008). The microvesicles also contained microRNAs (miRNAs) which were found to be abundant in glioblastomas (Skog et al., 2008). Glioblastoma-derived microvesicles were also found to potently promote angiogenic features in primary human brain microvascular endothelial cells (HBMVEC) in culture. This angiogenic effect was mediated at least in part through angiogenic proteins present in the microvesicles (Skog et al., 2008). The nucleic acids found within these microvesicles, as well as other contents of the microvesicles such as angiogenic proteins, can be used as valuable biomarkers for tumor diagnosis, characterization and prognosis by providing a genetic profile. Contents within these microvesicles can also be used to monitor tumor progression over time by analyzing if other mutations are acquired during tumor progression as well as if the levels of certain mutations or gene expression increase or decrease over time or over a course of treatment.
[0059] Certain aspects of the present invention are based on another finding that most of the extracellular RNA in bodily fluid from a subject is contained within microvesicles and thus protected from degradation by ribonucleases (Skog et al., 2008). More than 90% of extracellular RNA in total serum can be recovered in microvesicles (Skog et al., 2008).
[0060] One aspect of the present invention relates to methods for detecting, diagnosing, monitoring, treating or evaluating a disease or other medical condition in a subject comprising the steps of, isolating exosomes from a bodily fluid of a subject, and analyzing one or more nucleic acids contained within the exosomes. The nucleic acids are analyzed qualitatively and/or quantitatively, and the results are compared to results expected or obtained for one or more other subjects who have or do not have the disease or other medical condition. The presence of a difference in microvesicular nucleic acid content of the subject, as compared to that of one or more other individuals, can indicate the presence or absence of, the progression of (e.g., changes of tumor size and tumor malignancy), or the susceptibility to a disease or other medical condition in the subject.
[0061] The isolation methods and techniques described herein provide the following heretofore unrealized advantages: 1) the opportunity to selectively analyze disease- or tumor- specific nucleic acids, which may be realized by isolating disease- or tumor- specific microvesicles apart from other microvesicles within the fluid sample; 2) significantly higher yield of nucleic acid species with higher sequence integrity as compared to the yield/integrity obtained by extracting nucleic acids directly from the fluid sample; 3) scalability, e.g. to detect nucleic acids expressed at low levels, the sensitivity can be increased by isolating more microvesicles from a larger volume of serum; 4) purer nucleic acids in that protein and lipids, debris from dead cells, and other potential contaminants and PCR inhibitors are excluded from the microvesicle preparation before the nucleic acid extraction step; and 5) more choices in nucleic acid extraction methods as microvesicle preparations are of much smaller volume than that of the starting serum, making it possible to extract nucleic acids from the microvesicle preparations using small volume column filters.
[0062] The microvesicles are preferably isolated from a bodily fluid from a subject.
As used herein, a "bodily fluid" refers to a sample of fluid isolated from anywhere in the body of the subject, preferably a peripheral location, including but not limited to, for example, blood, plasma, serum, urine, sputum, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, fluid of the respiratory, intestinal, and genitourinary tracts, tear fluid, saliva, breast milk, fluid from the lymphatic system, semen, cerebrospinal fluid, intra-organ system fluid, ascitic fluid, tumor cyst fluid, amniotic fluid and combinations thereof.
[0063] The term "subject" is intended to include all animals shown to or expected to have microvesicles. In particular embodiments, the subject is a mammal, a human or nonhuman primate, a dog, a cat, a horse, a cow, other farm animals, or a rodent (e.g. mice, rats, guinea pig etc.). The term "subject" and "individual" are used interchangeably herein.
[0064] Methods of isolating microvesicles from a biological sample are known in the art. For example, a method of differential centrifugation is described in a paper by Raposo et al. (Raposo et al., 1996) and a paper by Skog et. al.(Skog et al., 2008). Methods of anion exchange and/or gel permeation chromatography are described in US Patent Nos. 6,899,863 and 6,812,023. Methods of sucrose density gradients or organelle electrophoresis are described in U.S. Patent No. 7,198,923. A method of magnetic activated cell sorting
(MACS) is described in (Taylor and Gercel-Taylor, 2008). A method of nanomembrane ultrafiltration is described in (Cheruvanky et al., 2007). Additionally, microvesicles can be identified and isolated from bodily fluid of a subject by a recently developed microchip technology that uses a microfluidic platform to separate tumor-derived microvesicles. This technology, as described in a paper by Nagrath et al. (Nagrath et al., 2007), can be adapted to identify and separate microvesicles using similar principles of capture and separation as taught in the paper. Further, a method of isolating microvesicles from urine samples is described in a paper by Miranda et. al.(Miranda et al, 2010) and in PCT/US2010/042365 by Russo et. al., filed July 16, 2010 (expected to publish in 2011). Each of the foregoing references is incorporated by reference herein for its teaching of these methods.
[0065] In one embodiment, the microvesicles isolated from a bodily fluid are enriched for those originating from a specific cell type, for example, lung, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colorectal, breast, prostate, brain, esophagus, liver, placenta, fetus cells. Because the microvesicles often carry surface molecules such as antigens from their donor cells, surface molecules may be used to identify, isolate and/or enrich for microvesicles from a specific donor cell type (Al-Nedawi et al., 2008; Taylor and Gercel-Taylor, 2008). In this way, microvesicles originating from distinct cell populations can be analyzed for their nucleic acid content. For example, tumor (malignant and non- malignant) microvesicles carry tumor-associated surface antigens and may be detected, isolated and/or enriched via these specific tumor-associated surface antigens. In one example, the surface antigen is epithelial-cell-adhesion-molecule (EpCAM), which is specific to microvesicles from carcinomas of lung, colorectal, breast, prostate, head and neck, and hepatic origin, but not of hematological cell origin (Balzar et al., 1999; Went et al., 2004). In another example, the surface antigen is CD24, which is a glycoprotein specific to urine microvesicles (Keller et al., 2007). In yet another example, the surface antigen is selected from a group of molecules including CD70, carcinoembryonic antigen (CEA), EGFR, EGFRvIII and other variants, Fas ligand, TRAIL, tranferrin receptor, p38.5, p97 and HSP72. Additionally, tumor- specific microvesicles may be characterized by the lack of surface markers, such as CD80 and CD86.
[0066] The isolation of microvesicles from specific cell types can be accomplished, for example, by using antibodies, aptamers, aptamer analogs or molecularly imprinted polymers specific for a desired surface antigen. In one embodiment, the surface antigen is specific for a cancer type. In another embodiment, the surface antigen is specific for a cell type which is not necessarily cancerous. One example of a method of microvesicle separation based on cell surface antigen is provided in U.S. Patent No. 7,198,923. As described in, e.g., U.S. Patent Nos. 5,840,867 and 5,582,981, WO/2003/050290 and a publication by Johnson et al. (Johnson et al., 2008), aptamers and their analogs specifically bind surface molecules and can be used as a separation tool for retrieving cell type- specific microvesicles. Molecularly imprinted polymers also specifically recognize surface molecules as described in, e.g., US Patent Nos. 6,525,154, 7,332,553 and 7,384,589 and a publication by Bossi et al. (Bossi et al., 2007) and are a tool for retrieving and isolating cell type-specific microvesicles. Each of the foregoing reference is incorporated herein for its teaching of these methods.
[0067] It may be beneficial or otherwise desirable to extract the nucleic acid from the exosomes prior to the analysis. Nucleic acid molecules can be extracted from a microvesicle using any number of procedures, which are well-known in the art, the particular extraction procedure chosen being appropriate for the particular biological sample. In some instances, with some techniques, it may also be possible to analyze the nucleic acid without extraction from the microvesicle.
[0068] In one embodiment, the extracted nucleic acids, including DNA and/or RNA, are analyzed directly without an amplification step. Direct analysis may be performed with different methods including, but not limited to, nanostring technology. NanoString technology enables identification and quantification of individual target molecules in a biological sample by attaching a color-coded fluorescent reporter to each target molecule. This approach is similar to the concept of measuring inventory by scanning barcodes.
Reporters can be made with hundreds or even thousands of different codes allowing for highly multiplexed analysis. The technology is described in a publication by Geiss et al. (Geiss et al., 2008) and is incorporated herein by reference for this teaching.
[0069] In another embodiment, it may be beneficial or otherwise desirable to amplify the nucleic acid of the microvesicle prior to analyzing it. Methods of nucleic acid amplification are commonly used and generally known in the art, many examples of which are described herein. If desired, the amplification can be performed such that it is quantitative. Quantitative amplification will allow quantitative determination of relative amounts of the various nucleic acids, to generate a profile as described below.
[0070] In one embodiment, the extracted nucleic acid is RNA. Preferably, the RNA is reverse-transcribed into complementary DNA before further amplification. Such reverse transcription may be performed alone or in combination with an amplification step. One example of a method combining reverse transcription and amplification steps is reverse transcription polymerase chain reaction (RT-PCR), which may be further modified to be quantitative, e.g., quantitative RT-PCR as described in US Patent No. 5,639,606, which is incorporated herein by reference for this teaching.
[0071] Nucleic acid amplification methods include, without limitation, polymerase chain reaction (PCR) (US Patent No. 5,219,727) and its variants such as in situ polymerase chain reaction (US Patent No. 5,538,871), quantitative polymerase chain reaction (US Patent No. 5,219,727), nested polymerase chain reaction (US Patent No. 5,556,773), self-sustained sequence replication and its variants (Guatelli et al., 1990), transcriptional amplification system and its variants (Kwoh et al., 1989), Qb Replicase and its variants (Miele et al., 1983), cold-PCR (Li et al., 2008) or any other known nucleic acid amplification methods, followed by the detection of the amplified molecules using techniques known to those of skill in the art. Especially useful are those detection schemes designed for the detection of nucleic acid molecules if such molecules are present in very low numbers. The foregoing references are incoiporated herein for their teachings of these methods.
[0072] The analysis of nucleic acids present in the microvesicles is quantitative and/or qualitative. For quantitative analysis, the amounts (e.g., expression levels), either relative or absolute, of all or specific nucleic acids of interest within the microvesicles are measured with methods known in the art (described below). For qualitative analysis, all or specific species of nucleic acids of interest within the microvesicles, whether wild-type or variants, are identified with methods known in the art (described below).
[0073] A "profile" is used herein to refer to the result of a quantitative analysis, a qualitative analysis, or a combination of both. The analysis may be an analysis of the nucleic acids as well as other contents extracted from a biological sample, e.g., a microvesicle. In one embodiment, a profile of genes refers to one or more genetic aberrations of the genes.
Similarly, a profile of genes also refers to a signature of genes herein. [0074] A "genetic aberration" is used herein to refer to a nucleic acid amount as well as a nucleic acid variant within a biological sample, e.g., a microvesicle. Specifically, genetic aberrations include, without limitation, over-expression of a gene (e.g., oncogenes) or a panel of genes, under-expression of a gene (e.g., tumor suppressor genes such as p53 or RB) or a panel of genes, alternative production of splice variants of a gene or a panel of genes, gene copy number variants (CNV) (e.g. DNA double minutes) (Hahn, 1993), nucleic acid modifications (e.g., methylation, acetylation and phosphorylations), single nucleotide polymorphisms (SNPs), chromosomal rearrangements (e.g., inversions, deletions and duplications), and mutations (insertions, deletions, duplications, missense, nonsense, synonymous or any other nucleotide changes) of a gene or a panel of genes, which mutations, in many cases, ultimately affect the activity and function of the gene products, lead to alternative transcriptional splicing variants and/or changes of gene expression level.
[0075] The determination of such genetic aberrations can be performed by a variety of techniques known to the skilled practitioner. For example, expression levels of nucleic acids, alternative splicing variants, chromosome rearrangement and gene copy numbers can be determined by microarray analysis (US Patent Nos. 6,913,879, 7,364,848, 7,378,245, 6,893,837 and 6,004,755) and quantitative PCR. Particularly, copy number changes may be detected with the Illumina Infinium II whole genome genotyping assay or Agilent Human Genome CGH Microarray (Steemers et al., 2006). Nucleic acid modifications can be assayed by methods described in, e.g., US Patent No. 7,186,512 and patent publication WO
2003/023065. Particularly, methylation profiles may be determined by Illumina DNA Methylation OMA003 Cancer Panel. SNPs and mutations can be detected by hybridization with allele- specific probes, enzymatic mutation detection, chemical cleavage of mismatched heteroduplex (Cotton et al., 1988), ribonuclease cleavage of mismatched bases (Myers et al., 1985), mass spectrometry (US Patent Nos. 6,994,960, 7,074,563, and 7,198,893), nucleic acid sequencing, single strand conformation polymorphism (SSCP) (Orita et al., 1989), denaturing gradient gel electrophoresis (DGGE)(Fischer and Lerman, 1979a; Fischer and Lerman, 1979b), temperature gradient gel electrophoresis (TGGE) (Fischer and Lerman, 1979a;
Fischer and Lerman, 1979b), restriction fragment length polymorphisms (RFLP) (Kan and Dozy, 1978a; Kan and Dozy, 1978b), oligonucleotide ligation assay (OLA), allele-specific PCR (ASPCR) (US Patent No. 5,639,611), ligation chain reaction (LCR) and its variants (Abravaya et al., 1995; Landegren et al., 1988; Nakazawa et al., 1994), flow-cytometric heteroduplex analysis (WO/2006/113590) and combinations or modifications of any of the foregoing. Notably, gene expression levels may be determined by the serial analysis of gene expression (SAGE) technique (Velculescu et al., 1995). In general, the methods for analyzing genetic aberrations are reported in numerous publications, not limited to those cited herein, and are available to skilled practitioners. The appropriate method of analysis will depend upon the specific goals of the analysis, the condition and/or history of the patient, and the specific cancer(s), diseases or other medical conditions to be detected, monitored or treated. The forgoing references are incorporated herein for their teachings of these methods.
[0076] In one embodiment, the analysis is of a profile of the amounts (levels) of all or specific nucleic acids present in the microvesicle, herein referred to as a "quantitative nucleic acid profile" of the micro vesicles. In another embodiment, the analysis is of a profile of the species of all or specific nucleic acids present in the microvesicles (both wild type as well as variants), herein referred to as a "nucleic acid species profile." A term used herein to refer to a combination of these types of profiles is "genetic profile" which refers to the determination of the presence or absence of nucleotide species, variants and also increases or decreases in nucleic acid levels. [0077] Once generated, these genetic profiles of the microvesicles are compared to those expected in, or otherwise derived from a healthy normal individual. A profile can be a genome-wide profile (representing all possible expressed genes or DNA sequences). It can be narrower as well, such as a cancer-wide profile (representing all possible genes or nucleic acids derived from or associated with cancer). Where a specific cancer is suspected or known to exist, the profile can be specific to that cancer (e.g., representing all possible genes or nucleic acids derived from or associated with the cancer or various clinically distinct subtypes of that cancer or known drug -resistant or sensitive forms of the cancer).
[0078] The methods of nucleic acid isolation, amplification and analysis are routine for one skilled in the art and examples of protocols can be found, for example, in Molecular Cloning: A Laboratory Manual (3-Volume Set) Ed. Joseph Sambrook, David W. Russel, and Joe Sambrook, Cold Spring Harbor Laboratory, 3rd edition (January 15, 2001), ISBN:
0879695773. A particular useful protocol source for methods used in PCR amplification is PCR Basics: From Background to Bench by Springer Verlag; 1st edition (October 15, 2000), ISBN: 0387916008.
[0079] Many methods of diagnosis performed on a tumor biopsy sample can be performed with microvesicles since tumor cells are known to shed microvesicles into bodily fluid and the genetic aberrations within these microvesicles are reflective of those within the tumor cells themselves (Skog et al., 2008). Furthermore, methods of diagnosis using microvesicles have characteristics that are absent in methods of diagnosis performed directly on a tumor biopsy sample. For example, one particular advantage of the analysis of microvesicular nucleic acids, as opposed to other forms of sampling of tumor/cancer nucleic acid, is the availability for analysis of tumor/cancer nucleic acids derived from all foci of a tumor or genetically heterogeneous tumors present in an individual. Biopsy samples are limited in that they provide information only about the specific focus of the tumor from which the biopsy is obtained. Different tumorous/cancerous foci found within the body, or even within a single tumor often have different genetic profiles, all of which are not analyzed in a standard biopsy. However, analysis of the microvesicular nucleic acids from an individual has the potential to provide a sampling of all foci within an individual. This provides valuable information with respect to recommended treatments, treatment
effectiveness, disease prognosis, and analysis of disease recurrence, which cannot be provided by a simple biopsy.
[0080] Aspects of the present invention relate to a method for monitoring disease (e.g. cancer) progression in a subject, and also to a method for monitoring disease recurrence in an individual. These methods comprise the steps of isolating microvesicles from a bodily fluid of an individual, as discussed herein, and analyzing nucleic acid within the microvesicles as discussed herein (e.g. to create a genetic profile of the microvesicles). The presence or absence of a certain genetic aberration or profile is used to indicate the presence or absence of the disease (e.g., cancer) in the subject as discussed herein. The process is performed periodically over time, and the results reviewed, to monitor the progression or regression of the disease, or to determine recurrence of the disease. Put another way, a change in the microvesicular genetic profile indicates a change in the disease state in the subject. The period of time to elapse between sampling of microvesicles from the subject, for performance of the isolation and analysis of the microvesicles, will depend upon the circumstances of the subject, and is to be determined by the skilled practitioner. Such a method would be extremely beneficial when analyzing nucleic acid from a gene that is associated with the therapy undergone by the subject. For example, a gene which is targeted by the therapy can be monitored for the development of mutations which make it resistant to the therapy, upon which time the therapy can be modified accordingly. The monitored gene may also be one which indicates specific responsiveness to a specific therapy.
[0081] Aspects of the present invention also relate to the fact that a variety of non- cancer diseases and/or medical conditions also have genetic links and/or causes, and such diseases and/or medical conditions can likewise be diagnosed and/or monitored by the methods described herein. Many such diseases are metabolic, infectious or degenerative in nature. One such disease is diabetes (e.g. diabetes insipidus) in which the vasopressin type 2 receptor (V2R) is modified. Another such disease is kidney fibrosis in which genetic profiles for the genes of collagens, fibronectin and TGF-β are changed. Changes in genetic profiles due to substance abuse, viral and/or bacterial infection, and hereditary disease states can likewise be detected by the methods described herein.
[0082] Diseases or other medical conditions for which the inventions described herein are applicable include, but are not limited to, nephropathy, diabetes insipidus, diabetes mellitus, diabetes type I, diabetes II, renal disease glomerulonephritis, bacterial or viral glomerulonephritides, IgA nephropathy, Henoch-Schonlein Purpura, membranoproliferative glomerulonephritis, membranous nephropathy, Sjogren's syndrome, nephrotic syndrome minimal change disease, focal glomerulosclerosis and related disorders, acute renal failure, acute tubulointerstitial nephritis, pyelonephritis, GU tract inflammatory disease, Pre- clampsia, renal graft rejection, leprosy, reflux nephropathy, nephrolithiasis, genetic renal disease, medullary cystic, medullar sponge, polycystic kidney disease, autosomal dominant polycystic kidney disease, autosomal recessive polycystic kidney disease, tuberous sclerosis, von Hippel-Lindau disease, familial thin-glomerular basement membrane disease, collagen III glomerulopathy, fibronectin glomerulopathy, Alport's syndrome, Fabry's disease, Nail- Patella Syndrome, congenital urologic anomalies, monoclonal gammopathies, multiple myeloma, amyloidosis and related disorders, febrile illness, familial Mediterranean fever, HIV infection- AIDS, inflammatory disease, systemic vasculitides, polyarteritis nodosa, Wegener's granulomatosis, polyarteritis, necrotizing and crecentic glomerulonephritis, polymyositis-dermatomyositis, pancreatitis, rheumatoid arthritis, systemic lupus
erythematosus, gout, blood disorders, sickle cell disease, thrombotic thrombocytopenia purpura, Fanconi's syndrome, transplantation, acute kidney injury, irritable bowel syndrome, hemolytic-uremic syndrome, acute corticol necrosis, renal thromboembolism, trauma and surgery, extensive injury, burns, abdominal and vascular surgery, induction of anesthesia, side effect of use of drugs or drug abuse, circulatory disease myocardial infarction, cardiac failure, peripheral vascular disease, hypertension, coronary heart disease, non-atherosclerotic cardiovascular disease, atherosclerotic cardiovascular disease, skin disease, psoriasis, systemic sclerosis, respiratory disease, COPD, obstructive sleep apnoea, hypoia at high altitude or endocrine disease, or acromegaly.
[0083] Selection of an individual from whom the microvesicles are isolated is performed by the skilled practitioner based upon analysis of one or more of a variety of factors. Such factors for consideration are whether the subject has a family history of a specific disease (e.g., a cancer), has a genetic predisposition for such a disease, has an increased risk for such a disease, or has physical symptoms which indicate a predisposition, or environmental reasons. Environmental reasons include lifestyle, exposure to agents which cause or contribute to the disease such as in the air, land, water or diet. In addition, having previously had the disease, being currently diagnosed with the disease prior to therapy or after therapy, being currently treated for the disease (undergoing therapy), being in remission or recovery from the disease, are other reasons to select an individual for performing the methods. [0084] The cancer diagnosed, monitored or otherwise profiled, can be any kind of cancer. This includes, without limitation, epithelial cell cancers such as lung, ovarian, cervical, endometrial, breast, brain, colon and prostate cancers. Also included are
gastrointestinal cancer, head and neck cancer, non- small cell lung cancer, cancer of the nervous system, kidney cancer, retina cancer, skin cancer, liver cancer, pancreatic cancer, genital-urinary cancer and bladder cancer, melanoma, and leukemia. In addition, the methods and compositions of the present invention are equally applicable to detection, diagnosis and prognosis of non-malignant tumors in an individual (e.g., neurofibromas, meningiomas and schwannomas).
[0085] In one embodiment, the cancer is brain cancer. Types of brain tumors and cancer are well known in the art. Glioma is a general name for tumors that arise from the glial (supportive) tissue of the brain. Gliomas are the most common primary brain tumors. Astrocytomas, ependymomas, oligodendrogliomas, and tumors with mixtures of two or more cell types, called mixed gliomas, are the most common gliomas. The following are other common types of brain tumors: Acoustic Neuroma (Neurilemmoma, Schwannoma.
Neurinoma), Adenoma, Astracytoma, Low-Grade Astrocytoma, giant cell astrocytomas, Mid- and High-Grade Astrocytoma, Recurrent tumors, Brain Stem Glioma, Chordoma, Choroid Plexus Papilloma, CNS Lymphoma (Primary Malignant Lymphoma), Cysts, Dermoid cysts, Epidermoid cysts, Craniopharyngioma, Ependymoma Anaplastic ependymoma,
Gangliocytoma (Ganglioneuroma), Ganglioglioma, Glioblastoma Multiforme (GBM), Malignant Astracytoma, Glioma, Hemangioblastoma, Inoperable Brain Tumors, Lymphoma, Medulloblastoma (MDL), Meningioma, Metastatic Brain Tumors, Mixed Glioma,
Neurofibromatosis, Oligodendroglioma. Optic Nerve Glioma, Pineal Region Tumors, Pituitary Adenoma, PNET (Primitive Neuroectodermal Tumor), Spinal Tumors,
Subependymoma, and Tuberous Sclerosis (Bourneville's Disease). [0086] As an exemplary embodiment of the present invention, one aspect of the present invention is a method of analyzing RNA profiles using microvesicles isolated from brain cancer serum samples. The method comprises the steps of isolating microvesicles from brain cancer serum samples and analyzing nucleic acids extracted from the isolated microvesicles.
[0087] As an exemplary embodiment of the present invention, another aspect of the present intention is the discovery of a series of brain cancer gene expression profiles or signatures. The signatures were discovered by analyzing nucleic acids extracted from brain cancer serum samples. The signatures can be used for the diagnosis and /or prognosis of brain caner, as well as treatment plan evaluation, selection and monitoring of brain cancer.
[0088] The exemplary embodiment of the present invention is illustrated in the following example for both method and signature aspects. In this example, gene signatures for glioblastoma cancer were obtained using methods and materials detailed below.
[0089] Blood samples from patients diagnosed with de-novo primary GBM were collected immediately prior to surgery, before opening of the dura mater, into a BD
Vacutainer SST (#367985) at Massachusetts General Hospital (MGH). Blood from normal healthy controls was collected from volunteers recruited at the MGH blood bank. All samples were collected with informed consent according to the appropriate protocols approved by the Institutional Review Board at MGH. The blood was left to clot for 30 min and serum was isolated according to manufacturer's recommendations within two hours of collection. Serum was filtered by slowly passing it through a 0.8 μιη syringe filter, aliquoted into 1.8 milliliter (ml) cryotubes and kept at -80°C until used. Altogether, 9 serum samples from glioblastoma patients and 7 serum samples from non-glioblastoma human subjects were obtained for the following analysis. [0090] Isolation of microvesicles from serum samples was performed as previously described (Skog et al., 2008). Briefly, 1 ml serum was centrifuged for 10 min at 300 x g to eliminate any cell contamination. Supernatants were further centrifuged for 20 min at 16,500 x g and filtered through a 0.22 μπι filter. Microvesicles were then pelleted by
ultracentrifugation at 110,000 x g for 70 min. The microvesicle pellets were washed in 13 ml PBS, pelleted again and resuspended in cold PBS. Isolated microvesicles were measured for their total protein content using DC Protein Assay (Bio-Rad, Hercules, CA, USA).
[0091] For the extraction of RNA from microvesicles, the pelleted microvesicles were incubated in an RNAse inhibitor solution for 5-10 minutes at room temperature. The RNase inhibitor can be from various known vendors, e.g., one inhibitor is "SUPERase" from
Ambion Inc. Total RNA was extracted from the RNAse-treated microvesicles using various commercial RNA extraction kits such as the QIAamp RNA Blood Mini Kit or the miRNeasy mini kit from Qiagen, or the MirVana RNA isolation kit from Ambion Inc., according to the manufacturer's protocols. After treatment with DNAse according to the manufacturers' protocol, total RNA was eluted in 30 ul nuclease-free water. RNA quality and concentration was assessed with the Agilent Bioanalyzer RNA Pico Chip yielding typical concentrations of 0.4-0.8ng^L for normal controls and 0.8-2.0ng^L for GBM patients.
[0092] The extracted RNA was then analyzed using the Agilent 44K Whole Human
Genome Oligo Microarrays (one-color), a standard gene expression analysis tool, according to standard protocols. Briefly, for the linear T7-based amplification step, from 0.07 μg up to 0.46 (.ig of total RNA was used, depending on the available amount of total RNA. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies). The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.5 -1.65 μg of Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile. Fluorescence signals of the hybridized Agilent
Microarrays were detected using Agilent's Microarray Scanner System (Agilent
Technologies).
[0093] The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For the determination of differential gene expression, FES -derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta
Biosoftware). This software offers - among other features - the ability to compare two single intensity profiles in a ratio experiment. All samples were labeled with Cy3. Here, the ratio experiments are designated as control versus (vs.) sample experiments (automated data output of the Resolver system).
[0094] The raw data from Feature Extraction was pre-processed and normalized in several different ways using R/Bioconductor and the packages limma, Agi4x44PrePro ess and vsn. To ensure that the normalization procedure did not introduce unintended biases or artifacts, the data was normalized in three different ways using Quartile normalization with and without background subtraction and variance stabilized normalization (VSN), and the normalized data was compared to the raw values. Normalized data was transferred to Excel and filtered with different criteria as described below. Gene lists of interest were uploaded and analyzed with the online Gene Ontology Tool DAVID 6.7
(http ://david. abcc.ncifcrf.gov/) .
[0095] As a result, microvesicles (less than 0.8 μπι in diameter) were isolated from serum samples from 9 GBM patients (prior to surgery) and 7 normal healthy controls. RNA from this exosomal fraction (exoRNA) was extracted, labeled and amplified by linear amplification and hybridized to Agilent 4x44K arrays. The raw data was corrected for background, normalized and submitted for deposit in the Gene Expression Omnibus database by user name/ID Mikkell Noerholm on September 4, 2010 in the format of GEOarchive. The deposited file name is AgilentQuartileNorm_MeanSignal_GBMvsCTRL_GEO.zip. The deposited data are here incorporated by reference in its entirety including the array oligo sequences.
[0096] Clustering analysis, heat maps, and Principle Component Analysis of the normalized data was performed by using various softwares, e.g. GeneSifter, provided various sources, e.g., dChip (http://biosunl.harvard.edu/complab/dchip). A clustering analysis for genome-wide expression data from DNA microarray hybridization uses standard statistical algorithms to cluster genes according to similarity in pattern of gene expression (Eisen et al., 1998). A type of Principle Component Analysis is described previously (Alter et al., 2000).
[0097] Other data analysis tools, known in the art, may be substituted for the tools described and exemplified herein. In addition to Clustering Analysis, Principle Component Analysis, other analytic tools such as Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis (Zweig and Campbell, 1993), Binary Analysis (US Patent No. 7,081,340), Cox Proportional Hazards Analysis (US Patent No. 7,081,340), Support Vector Machines and Recursive Feature Elimination (SVM-RFE) (US Patent No. 7,117,188), Classification to Nearest Centroid (Dabney, 2005) or combinations thereof may be used to analyze the expression data including microarray data.
[0098] We conducted a t-test between the two groups of samples on each gene in the full data set to identify the genes that best separate, distinguish, or discriminate between the two groups. As shown in Figure 17, a volcano plot of the p-values against the level of differential expression, it is evident that substantially more genes are significantly down- regulated than up-regulated in the GBM samples. The level of differential expression is the difference of the median expression levels in the GBM and Control groups (i.e., median level in GBM - median level in Control). The typical degree of disregulation and the significance (p-value) is also higher for the down-regulated genes than for the up-regulated genes.
[0099] Based on the p values and the level of differential expression, we derived 16 different groups of genes from the above microarray data. The 16 groups of genes are listed in Tables 1-16, respectively. The criteria for inclusion of the each gene in the groups in Tables 1-16 are as follows:
Table 1: p < 5xl0~4 and with the log-median-ratio being at least "1" or above, or p < 0.000002;
Table 2: p < 5x104 and the log-median-ratio being at least "1" or above;
Table 3: p < 2xl0"3 and the log-median-ratio being at least "1" or above;
Table 4: p < 2xl0"6;
Table 5: p < lxl0"5;
Table 6: p < 5xl0"4 and the log-median-ratio being at least "0.8" or above, or being at least "-0.8" or below; Table 7: p < lxlO"5 and the log-median-ratio being at least "0.585" or above, or being at least "-0.585" or below;
Table 8: p < lxlO"4 and the log-median-ratio being at least "1" or above, or being at least or below;
Table 9: p < lxlO"5 and the log-median-ratio being below "0";
Table 10: p < lxlO"5 and log-median-ratio being above "0";
Table 11: p < lxlO"4;
Table 12: p < lxlO"3 and the log-median-ratio being at least "1" or above, or being or below;
Table 13: p < 0.05 and the log-median-ratio being at least "1" or above, or being or below;
Table 14: p < 0.05 and the log-median-ratio being at least "0.585" or above;
Table 15: p < 0.05 and the log-median-ratio being at least "1" or above; and
Table 16: p < 0.001.
[00100] Each of the 16 groups can be a gene signature for glioblastoma. We tested each group for its capability as a glioblastoma signature. For each group, two independent tests were performed. One test used Clustering Analysis. The other test used Principle Component Analysis. For each group, the results (as illustrated in Figures 1-16, As and Bs, respectively) showed that at least one of the two tests separated the cancer group and the control group.
[00101] Accordingly, one embodiment of the present invention is a profile of one or more of genes selected from the genes in Tables 1-16. In another embodiment, the profiles are of one or more genes selected from a single Table, e.g., from Table 1. In a further embodiment, the profiles are of a group of genes comprising each of the genes in a single Table, e.g., Tablel. One or more members in each group constitute a glioblastoma gene signature because either Clustering Analysis or Principle Component Analysis of the expression profiles of such one or more members in each group can separate the disease and control samples.
[00102] Another embodiment of the present invention is a method of applying the signatures for aiding the diagnosis, prognosis or therapy treatment for a subject. The method comprises first isolating microvesicles from the subject, measuring the expression levels of one or more RNA transcripts extracted from isolated microvesicles, determining a test profile of one or more RNA transcripts based on the measured expression level(s), and comparing the test profile to a reference profile to determine the characteristics of the test profile.
[00103] For example, as shown in Table 1, the group included 22 genes based on the inclusion criteria of p<5xl0~4 and a log-median-ratio being at least "1" or above, or p<0.000002. The 22 genes have functionalities including as receptors, transcription factors, and enzymes. As shown in Figures 1A, the 22-gene signature clusters control samples together in one subgroup and disease samples together in another subgroup when subjected to a Clustering Analysis. The disease samples GBM11, GBM12, GBM13, GBM15, GBM16, GBM17, GBM18, GBM19, and GBM20 cluster together in one subgroup. The control samples from non-Glioblastoma human subjects, Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8, clustered in another subgroup. The separation of GBM and Control samples can be achieved by Clustering Analysis. As shown in Figure IB, the same 22-gene signature is validated using Principle Component Analysis. The Control group dots appear on the upper left side of the plot while the GBM group dots appear on the middle-right side of the plot.
[00104] Furthermore, an evidence-based analysis tool, optionally together with one or more of the Heuristic methods described above, may also be used for analyzing expression data. For example, a gene ontology analysis may be carried out and genes in the same biological signaling pathway group together. A signature or profile comprised of a group of genes in a relevant signaling pathway may be derived and used for the purpose of diagnosing a corresponding biological condition.
[00105] As a further analytical step, we performed a multiple testing correction analysis in which a normalized data set was subjected to an unpaired t-test. The p-values were corrected using the Benjamin and Hochberg Method (Benjamini and Hochberg, 1995) with a cut-off of corrected p<0.05 and fold change of >2.5. As a result of the application of this method, 275 genes were found to be down-regulated. Using the above-mentioned criteria, a Gene Ontology (GO) analysis with an enrichment score of 64.26 showed that 210 recognized genes had GO terms related to Translation elongation, Ribosome, or
ribonucleoprotein. Furthermore, 24 genes were found to be upregulated. Using the above- mentioned criteria, a GO analysis with an enrichment score of 1.27 showed that 23 recognized genes had GO terms related to transcription (i.e. transcription factor activity, transcription, DNA binding, homeobox).
[00106] Based on the p values that have been corrected using the Benjamin and
Hochberg Method and the level of differential expression, we derived 4 additional groups of genes from the above microarray data. The 4 groups of genes are listed in Tables 17-20, respectively. The criteria to obtain the groups in Tables 17-20 are as follows:
Table 17: p<5xl0~2 and with the log-median-ratio being at least "1" or above, or being at least or below;
Table 18: p<5xl0~2 and the log-median-ratio being at least "1" or above, or being at least "- 1.5" or below; Table 19: p<5xl0~2 and the log-median-ratio being at least "1" or above;
Table 20: p<5xl0~2 and the log- median-ratio being at least "-1.5" or below,
respectively.
[00107] Each of the 4 groups can be a gene signature for glioblastoma. We tested each group for its capability as a glioblastoma signature. For each group, two independent tests were performed. One test used Clustering Analysis. The other test used Principle
Component Analysis. For each group, the results (as illustrated in Figures 18-21 As and Bs, respectively) showed that at least one of the two tests can separate the cancer group and the control group.
[00108] For example, as shown in Table 18, the group includes 31 genes based in the inclusion criteria of p<5xl0~ and the log- median-ratio being at least "1" or above, or being at least "-1.5" or below. The 31 genes have various functionalities including as receptors, transcription factors, and enzymes. As shown in Figures 19A, the 31 -gene signature clusters control samples together in one subgroup and disease samples together in another subgroup when subjected to Clustering Analysis. The 9 tumor samples are easily distinguishable from and clearly form a cluster different from the 7 Normal Controls. The disease samples GBM11, GBM12, GBM13, GBM15, GBM16, GBM 17, GBM18, GBM19, and GBM20 cluster together in one subgroup. The control samples from non-Glioblastoma human subjects, Ctrll, Ctrl2, Ctrl3, Ctrl4, Ctrl5, Ctrl7 and Ctrl8, clustered in another subgroup. The separation of GBM and Control samples can be achieved by Clustering Analysis. As shown in Figure 19B, the same 31 -genes signature was validated using Principle Component Analysis. The Control group dots appear on the upper left side of the plot. The GBM group dots appear on the middle-right side of the plot. [00109] All patents, patent applications, and publications identified are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents.
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[00110] While the present invention has been disclosed with reference to certain embodiments, numerous modifications, alterations, and changes to the described embodiments are possible without departing from the scope of the present invention, as defined in the appended claims. Accordingly, it is intended that the present invention not be limited to the particular described embodiments, but that it enjoy the full scope defined by the language of the following claims, and equivalents thereof.
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Claims

What is claimed is:
1. A profile of one or more RNA transcripts obtained from microvesicles, wherein the one or more RNA transcripts are selected from Tables 1-20.
2. The profile of claim 1, wherein the microvesicles are isolated from a bodily fluid from a subject.
3. The profile of claim 2, wherein the bodily fluid is blood, serum, plasma or urine.
4. The profile of claim 2, wherein the subject is a human subject.
5. The profile of claim 4, wherein the human subject is a brain cancer patient.
6. The profile of claim 5, wherein the brain cancer is glioblastoma.
7. The profile of claim 1, wherein the profile is obtained through analyzing RNA
transcripts obtained from microvesicles.
8. The profile of claim 7, wherein the analysis of RNA transcripts is performed by a method comprising microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination thereof.
9. The profile of claim 8, wherein the analytic method further comprises data analysis.
10. The profile of claim 9, wherein the data analysis comprises Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis, Binary Analysis, Cox Proportional Hazards Analysis, Support Vector Machines and Recursive Feature Elimination (SVM-RFE),
Classification to Nearest Centroid, Evidence-based Analysis, or a combination thereof.
11. The profile of claim 10, wherein the data analysis comprises Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, or a combination thereof.
12. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 1.
13. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 1.
14. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 2.
15. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 2.
16. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 3.
17. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 3.
18. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 4.
19. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 4.
20. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 5.
21. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 5.
22. The profile claim I, wherein the one or more RNA transcripts are selected from Table 6.
23. The profile of claim 1, wherein the one or more RNAs transcripts comprise each of the transcripts in Table 6.
24. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 7.
25. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 7.
The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 8.
The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 8.
The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 9.
The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 9.
The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 10.
The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 10.
The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 11.
The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 11.
The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 12.
The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 12.
The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 13.
The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 13.
The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 14.
39. The profile of claim 1, wherein the one or more RNA transcript comprise each of the transcripts in Table 14.
40. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 15.
41. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 15.
42. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 16.
43. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 16.
44. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 17.
45. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 17.
46. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 18.
47. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 18.
48. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 19.
49. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 19.
50. The profile of claim 1, wherein the one or more RNA transcripts are selected from Table 20.
51. The profile of claim 1, wherein the one or more RNA transcripts comprise each of the transcripts in Table 20.
52. A method of aiding diagnosis, prognosis or therapy treatment planning for a subject, comprising: a. isolating microvesicles from a subject; b. measuring the expression level of one or more RNA transcripts extracted from the isolated microvesicles; c. determining a profile of the one or more RNA transcripts based on the
expression level; and d. comparing the profile to a reference profile to aid diagnosis, prognosis or therapy treatment planning for the subject.
53. The method of claim 52, wherein the microvesicles are isolated from a bodily fluid from the subject.
54. The method of claim 53, wherein the bodily fluid is blood, plasma, serum or urine.
55. The method of claim 53, wherein the subject is a human subject.
56. The method of claim 55, wherein the human subject is a brain cancer patient.
57. The method of claim 55, wherein the brain cancer is glioblastoma.
58. The method of claim 52, wherein step (b) is performed by a method comprising microarray analysis, Reverse Transcription PCR, Quantitative PCR or a combination thereof.
59. The method of claim 52, wherein step (c) performed by a method of data analysis.
60. The method of claim 59, wherein the data analysis comprises Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, Receiver Operating Characteristic Curve Analysis, Binary Analysis, Cox Proportional Hazards Analysis, Support Vector Machines and Recursive Feature Elimination (SVM-RFE),
Classification to Nearest Centroid, Evidence-based Analysis, or a combination thereof.
61. The method of claim 60, wherein the data analysis comprises Clustering Analysis, Principle Component Analysis, Linear Discriminant Analysis, or a combination thereof.
62. The method of claim 52, wherein the one or more RNA transcripts are selected from Tables 1-16.
63. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 1.
64. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 1.
65. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 2.
66. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 2.
67. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 3.
68. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 3.
69. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 4.
70. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 4.
71. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 5.
72. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 5.
73. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 6.
74. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 6.
75. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 7.
76. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 7.
77. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 8.
78. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 8.
79. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 9.
80. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 9.
81. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 10.
82. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 10.
83. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 11.
84. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 11.
85. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 12.
86. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 12.
87. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 13.
88. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts in Table 13.
89. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 14.
90. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 14.
91. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 15.
92. The method in claim 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 15.
93. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 16.
94. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 16.
95. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 17.
96. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 17.
97. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 18.
98. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 18.
99. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 19.
100. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 19.
101. The method of claim 52, wherein the one or more RNA transcripts are selected from Table 20.
102. The method of claim 52, wherein the one or more RNA transcripts comprise each of the transcripts from Table 20.
103. A method of preparing a personalized genetic profile report for a subject, comprising the steps of:
(a) isolating microvesicles from a subject;
(b) detecting or measuring one or more genetic aberrations within the isolated microvesicles;
(c) determining one or more genetic profiles from the data obtained from steps (a) and (b);
(d) optionally comparing the one or more genetic profiles to one or more
reference profiles; and
(e) creating a report summarizing the data obtained from steps (a) through (d) and optionally including diagnostic, prognostic or therapeutic treatment information.
104. The method of claim 103, wherein step (b) comprises the quantitative measurement of one or more nucleic acids within the isolated microvesicles and step (c) comprises the determination of one or more quantitative nucleic acid profiles.
105. The method of claim 104, wherein the one or more nucleic acids are RNA transcripts selected from Tables 1-20.
106. The method of claim 104, wherein the one or more nucleic acids are RNA transcripts selected from any one of Tables 1- 20.
107. The method of claim 104, wherein the one or more nucleic acids comprise each of the RNA transcripts in any one of Tables 1-20.
108. A kit for genetic analysis of an exosome preparation from a body fluid sample from a subject, comprising, in a suitable container, one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from Tables 1-20.
109. The kit of claim 108, comprising one or more reagents suitable for hybridizing to or amplifying one or more of the RNA transcripts selected from any one of Tables 1-20.
110. The kit of claim 108, comprising one or more reagents suitable for hybridizing to or amplifying each of the RNA transcripts in any one of Tables 1-20.
111. An oligonucleotide microarray for genetic analysis of an exosome preparation from a body fluid sample from a subject, wherein the oligos on the array are custom-designed to hybridize exclusively to one or more transcripts selected from Tables 1-20.
112. A method of identifying at least one potential biomarker for a disease or other medical condition, the method comprising:
(a) isolating microvesicles from subjects having a disease or other medical condition of interest and from subjects who do not have the disease or other medical condition of interest;
(b) measuring the expression level of a target RNA transcript extracted from the isolated microvesicles from each of the subjects;
(c) comparing the measured levels of the target RNA transcript from each of the subjects; and
(d) determining whether there is a statistically significant difference in the measured
levels;
113. The method of claim 112, wherein a determination resulting from step (d) of a
statistically significant difference in the measured levels identifies the target RNA transcript and its corresponding gene as potential biomarkers for the disease or other medical condition, and wherein the target RNA transcript is selected from Tables 1- 20.
114. A method of profiling genetic aberrations in a subject, comprising the steps of:
(a) isolating microvesicles from a subject;
(b) detecting or measuring one or more genetic aberrations within the isolated microvesicles;
(c) detei nining one or more genetic profiles from the data obtained from steps (a) and (b).
115. The method of claim 114, wherein step (b) comprises the quantitative measurement of one or more nucleic acids within the isolated microvesicles and step (c) comprises the determination of one or more quantitative nucleic acid profiles.
116. The method of claim 114, wherein the one or more nucleic acids are RNA transcripts selected from Tables 1-20.
117. The method of claim 114, wherein the one or more nucleic acids are RNA transcripts selected from any one of Tables 1- 20.
118. The method of claim 114, wherein the one or more nucleic acids comprise each of the RNA transcripts in any one of Tables 1-20.
119. The method of any of claims 52, 103, 112 or 114, further comprising the step of
enriching the isolated microvesicles for microvesicles originating from a specific cell type.
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