Methods for profiling and quantitating cell-free rna

Abstract

The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.

What is claimed is: 
     
         1 . A noninvasive method of quantifying circulating cell-free messenger RNA of a human test subject when the human test subject's central nervous system is at risk of being affected by Multiple Sclerosis comprising:
 (a) obtaining cell-free RNA from a sample of the human test subject;   (b) quantifying a sample level of a circulating cell-free messenger RNA in the cell-free RNA by subjecting the circulating cell-free messenger RNA to at least one process selected from the group consisting of: reverse transcription, polynucleotide amplification, sequencing, probe hybridization, and microarray hybridization, and quantifying a product of said at least one process;   wherein quantifying comprises detecting the proportion of the circulating cell-free messenger RNA that is contributed to the plasma sample by the central nervous system.   
     
     
         2 . The method of  claim 1 , comprising comparing the relative contribution of the at least one tissue to the plurality of RNA transcripts in the individual to a reference level of relative tissue RNA contribution, and identifying a risk of MS in the central nervous system when the relative contribution of the central nervous system to the plurality of RNA transcripts in the individual differs substantially from the reference level of relative tissue RNA contribution. 
     
     
         3 . The method of  claim 1 , comprising comparing the relative contribution of the at least one tissue to the plurality of RNA transcripts in the individual to a reference level of relative tissue RNA contribution, and concluding that there is a reduced risk of MS in the central nervous system when the relative contribution of the central nervous system to the plurality of RNA transcripts in the individual does not differ substantially from the reference level of relative tissue RNA contribution. 
     
     
         4 . The method of  claim 1 , wherein the fluid sample comprises blood. 
     
     
         5 . The method of  claim 4 , comprising depleting cells from the sample prior to quantifying. 
     
     
         6 . The method of  claim 1 , wherein the RNA is predominantly cell-free RNA. 
     
     
         7 . The method of  claim 6 , wherein the RNA is predominantly mRNA. 
     
     
         8 . The method of  claim 6 , wherein the RNA is mRNA. 
     
     
         9 . The method of  claim 1 , wherein the fluid sample comprises cerebrospinal fluid. 
     
     
         10 . The method of  claim 1 , wherein quantifying at least some of the RNA transcripts comprises obtaining sequence tags of at least a portion of the RNA transcripts. 
     
     
         11 . The method of  claim 1 , wherein quantifying at least some of the RNA transcripts comprises sequencing at least a portion of the RNA transcripts. 
     
     
         12 . The method of  claim 1 , wherein quantifying at least some of the RNA transcripts comprises amplifying at least a portion of the RNA transcripts. 
     
     
         13 . The method of  claim 1 , wherein the plurality of RNA transcripts comprises transcripts arising from at least two of cerebrum, cerebellum, dorsal root ganglion, superior cervical ganglion, pineal gland, amygdala, trigeminal ganglion, cerebral cortex, hypothalamus. 
     
     
         14 . The method of  claim 1 , wherein the plurality of RNA transcripts are expressed in healthy tissues. 
     
     
         15 . The method of  claim 1 , wherein the plurality of RNA transcripts are not implicated in a disease mechanism. 
     
     
         16 . The method of  claim 2 , wherein the reference level of relative tissue RNA contribution is obtained from a healthy control. 
     
     
         17 . The method of  claim 2 , comprising diagnosing the individual as having MS. 
     
     
         18 . The method of  claim 2 , wherein the reference level of relative tissue RNA contribution is obtained from the individual at a prior time point. 
     
     
         19 . The method of  claim 18 , comprising monitoring MS progression. 
     
     
         20 . The method of  claim 18 , comprising monitoring neurodegenerative toxicity. 
     
     
         21 . The method of  claim 2 , comprising initiating a surgical intervention.