Detection of infectious prion protein by seeded conversion of recombinant prion protein

Abstract

The present disclosure relates to methods and compositions for the detection of infectious proteins or prions in samples, including the diagnosis of prion related diseases. One embodiment is an ultrasensitive method for detecting PrP-res (PrP Sc ) that allows the use of recombinant PrP-sen (rPrP-sen) as a substrate for seeded polymerization. A sample is mixed with purified rPrP-sen to make a reaction mix which is incubated to permit aggregation of the rPrP-sen with the PrP-res that may be present in the sample. Any aggregates are intermittently disaggregated by agitation and the reaction allowed to proceed to amplify target substrate. Any rPrP-res (Sc) in the reaction mix is detected to indicate the presence of PrP-res in the original sample. In the QUIC method in, the reaction mixture is shaken intermittently. The surprising speed and efficiency of the method permits the rapid identification and diagnosis of prion disease.

1 . A method for detecting the protease resistant prion protein (PrP-res) in a sample comprising:
 (a) mixing the sample with the purified recombinant protease-sensitive prion protein (rPrP-sen) to make a reaction mix, wherein the rPrP-sen comprises the amino acid sequence set forth as SEQ ID NO: 3, the amino acid sequence set forth as SEQ ID NO: 4, or the amino acid sequence set forth as SEQ ID NO: 8;   (b) performing an amplification reaction comprising:
 (i) incubating the reaction mix at about 37 to 55° C. to permit coaggregation of the rPrP-sen with the PrP-res that may be present in the reaction mix, and maintaining incubation conditions that promote coaggregation of the rPrP-sen with the PrP-res and results in a conversion of the rPrP-sen to the recombinant protease resistant prion protein initiated by the presence of prions (rPrP-res (Sc) ), which is initiated by the presence of PrP-res in the sample, while inhibiting development of the spontaneously occurring recombinant prion protein (rPrP-res (spon) ); 
 (ii) agitating aggregates formed during step (i), in shaking cycles, wherein each shaking cycle of the shaking cycles comprises a period of rest and a period of shaking, and wherein the period of rest is about 30 seconds in length and the period of shaking is about 30 second in length, or wherein the period of rest is about 60 second in length and the period of shaking is about 60 seconds in length, wherein agitating is performed for about 2 to 48 hours in the absence of sonication; and 
   (c) detecting rPrP-res (Sc)  in the reaction mix, wherein detection of rPrP-res (Sc)  in the reaction mix indicates that PrP-res was present in the sample.   
     
     
         2 . The method of  claim 1 , wherein detecting the rPrP-res (Sc)  comprises detecting rPrP-res (Sc)  aggregates in the sample. 
     
     
         3 . The method of  claim 1 , wherein the method further comprises digesting the reaction mix with proteinase K prior to detecting rPrP-res (Sc)  in the reaction mix. 
     
     
         4 . The method of  claim 2 , wherein detecting rPrP-res (Sc)  comprises detecting rPrP-res (Sc)  with an antibody that specifically binds to prion protein. 
     
     
         5 . The method of  claim 4 , wherein the antibody is a polyclonal antibody. 
     
     
         6 . The method of  claim 4 , wherein the antibody is a monoclonal antibody. 
     
     
         7 . The method of  claim 1 , wherein steps (a) and (b) are repeated for approximately 48 hours. 
     
     
         8 . The method of  claim 1 , wherein the reaction mix is incubated at 45° C. to 55° C. 
     
     
         9 . The method of  claim 1 , wherein the reaction mix is incubated at 45° C. 
     
     
         10 . The method of  claim 1 , wherein the rPrP-sen consists of the amino acid sequence set forth as one of SEQ ID NO: 3, SEQ ID NO: 4 or SEQ ID NO: 8. 
     
     
         11 . The method of  claim 1 , wherein the sample is a tissue sample from an animal. 
     
     
         12 . The method of  claim 1 , wherein prion can be detected in a sample containing no more than about 1 fg PrP-res. 
     
     
         13 . The method of  claim 1 , wherein the method is a method of diagnosing a prion disease. 
     
     
         14 . The method of  claim 1 , wherein detecting rPrP-res (Sc)  in the reaction mix comprises the use of a fluorescence assay. 
     
     
         15 . A method for amplifying and detecting the human protease resistant prion protein (PrP-res) in a sample comprising:
 (a) mixing the sample with purified recombinant protease-sensitive prion protein (rPrP-sen) comprising a human rPrP-sen amino acid sequence, wherein the human rPrP-sen comprises the amino acid sequence forth as SEQ ID NO: 3 and SEQ ID NO: 4 to make a reaction mix;   (b) performing an amplification reaction comprising:   (i) incubating the reaction mix at about 37° C. to 55° C. to permit formation of aggregates of the recombinant rPrP-sen with the human PrP-res that may be present in the reaction mix, and maintaining incubation conditions that promote aggregation of the human rPrP-sen with the human PrP-res and results in a conversion of the human rPrP-sen to recombinant protease resistant prion protein initiated by the presence of prions (rPrP-res (Sc) ) while inhibiting development of the spontaneously occurring recombinant prion protein (rPrP-res (spon) );   (ii) agitating aggregates formed during step (i), in shaking cycles, wherein each shaking cycle of the shaking cycles comprises a period of rest and a period of shaking, and wherein the shaking cycle is from about 60 to 120 seconds in length, and wherein agitating is performed for about 2-48 hours in the absence of sonication;   (c) detecting rPrP-res (Sc)  in the reaction mix using fluorescence, wherein detection of rPrP-res (Sc)  in the reaction mix indicates that PrP-res was present in the sample.   
     
     
         16 . The method of  claim 15 , wherein the purified recombinant protease-sensitive prion protein (rPrP-sen) further comprises hamster rPrP-sen. 
     
     
         17 . The method of  claim 15 , wherein the hamster rPrP-sen comprises the amino acid sequence set forth as SEQ ID NO: 8. 
     
     
         18 . The method of  claim 15 , comprising incubating the reaction mix at about 37° C., 45° C. or 55° C. 
     
     
         19 . The method of  claim 15 , wherein the purified recombinant protease-sensitive prion protein (rPrP-sen) consists of the amino acid sequence set forth as SEQ ID NO: 3 or the amino acid sequence set forth as SEQ ID NO: 4. 
     
     
         20 . The method of  claim 15 , wherein the period of rest and the period of shaking are substantially equal.