Methods and systems for detecting tissue conditions

Abstract

Provided herein are methods and systems for detecting tissue conditions. In some aspects, levels of one or more markers of a disease or condition and one or more tissue-specific cell-free polynucleotides are quantified, levels are compared to a reference, and it is determined whether the tissue has been damaged by the disease or condition based on the comparing. Systems for performing the methods described herein are also provided.

What is claimed is: 
     
         1 . A method comprising:
 a) obtaining a blood sample from a subject;   b) removing cells from the blood sample to obtain a cell-depleted sample;   c) removing an extracellular microparticle from the blood sample to obtain a microparticle-depleted sample;   d) quantifying an amount of cell-free RNA corresponding to a gene in the microparticle-depleted sample.   
     
     
         2 . The method of  claim 1 , wherein the removing the extracellular microparticle comprises contacting the cell-depleted sample with a binding moiety that interacts with a protein on the surface the extracellular microparticle. 
     
     
         3 . The method of  claim 1 , wherein the binding moiety is an antibody or antigen-binding antibody fragment. 
     
     
         4 . The method of  claim 3 , wherein the antibody or antigen-binding antibody fragment interacts with a cell surface marker known to be expressed by a blood cell. 
     
     
         5 . The method of  claim 3 , wherein the antibody comprises an anti-CD45 antibody. 
     
     
         6 . The method of  claim 3 , wherein the antibody comprises an anti-CD66b antibody. 
     
     
         7 . The method of  claim 1 , comprising contacting the cell-depleted sample with a first antibody that interacts with a first protein on a first cell and a second antibody that interacts with a second protein on a second cell. 
     
     
         8 . The method of  claim 7 , wherein the first protein is not expressed on the second cell and the second protein is not expressed on the first cell. 
     
     
         9 . The method of  claim 1 , wherein the extracellular microparticle is an exosome. 
     
     
         10 . The method of  claim 9 , wherein the exosome is from a blood cell. 
     
     
         11 . The method of  claim 10 , wherein the blood cell is a platelet and wherein removing the extracellular microparticle comprises contacting the cell-depleted sample with an anti-GypA antibody or GypA antigen-binding fragment thereof. 
     
     
         12 . The method of  claim 10 , wherein the blood cell is a red blood cell and wherein removing the extracellular microparticle comprises contacting the cell-depleted sample with an anti-CD235a antibody or CD235a antigen-binding fragment thereof. 
     
     
         13 . The method of  claim 10 , wherein the blood cell is a granulocyte and wherein removing the extracellular microparticle comprises contacting the cell-depleted sample with an anti-CD66b antibody or CD66b antigen-binding fragment thereof. 
     
     
         14 . The method of  claim 10 , wherein the blood cell is a lymphocyte and wherein removing the extracellular microparticle comprises contacting the cell-depleted sample with an antibody or antigen-binding fragment thereof that binds CD45, CD19 or CD3. 
     
     
         15 . The method of  claim 1 , wherein the cell-depleted sample is incubated 1 h at 60 degrees Celsius. 
     
     
         16 . The method of  claim 15 , comprising incubating the cell-depleted sample in the presence of a chaotropic salt, detergent, proteinase K, 2-mercaptoethanol, or a combination thereof. 
     
     
         17 . The method of  claim 16 , comprising incubating the sample with Tris. 
     
     
         18 . The method  claim 1 , comprising disrupting lipidic and proteinaceous structures. 
     
     
         19 . The method of  claim 1 , comprising contacting the cell-depleted sample with a silica column. 
     
     
         20 . The method of  claim 19 , comprising incubating the cell-depleted sample with a chaotropic salt and 100% isopropanol to enhance the binding of RNA to the silica column.