Methods for detection of plasma cell dyscrasia

Abstract

The present invention is directed to methods for detecting a plasma cell dyscrasia like myeloma or MGUS, methods for determining whether a plasma cell dyscrasiais stable or progressive, methods for determining a risk for disease relapse, and methods for determining a response by a subject having a plasma cell dyscrasia to a therapy.

1 . A method for detecting a plasma cell dyscrasia in a subject in need thereof, comprising:
 determining the expression level of at least 32 biomarkers from a test sample from the subject by contacting the test sample with a plurality of agents specific to detect the expression of the at least 32 biomarkers, wherein the at least 32 biomarkers comprise ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2, MALAT1,MBNL1,MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, P1AS2, PRKAA1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, UBE2J1, and at least one housekeeping gene;   normalizing the expression level of each of ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2, MALAT1, MBNL1, MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, PJAS2, PRKAA1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, and UBE2J1 to the expression level of the at least one housekeeping gene, thereby obtaining a normalized expression level of each of ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2, MALAT1,MBNL1,MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, PJAS2, PRKAA1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, and UBE2J1;   inputting each normalized expression level into an algorithm to generate a score;   comparing the score with a first predetermined cutoff value; and   producing a report, wherein the report identifies the presence of a plasma cell dyscrasia in the subject when the score is equal to or greater than the first predetermined cutoff value or determining the absence of a plasma cell dyscrasia in the subject when the score is below the first predetermined cutoff value, wherein the first predetermined cutoff value is 20 on a scale of 0 to 100.   
     
     
         2 . The method of  claim 1 , wherein the plasma cell dyscrasia is monoclonal gammopathy of undetermined significance (MGUS) or myeloma. 
     
     
         3 . The method of  claim 1 , wherein the at least one housekeeping gene is selected from the group consisting of ALG9, SEPN, YWHAQ, VPS37A, PRRC2B, DOPEY2, NDUFB11, ND4, MRPL19, PSMC4, SF3A1, PUM1, ACTB, GAPD, GUSB, RPLP0, TFRC, MORF4L1, 18S, PPIA, PGK1, RPL13A, B2M, YWHAZ, SDHA, HPRT1, TOX4, and TPT1. 
     
     
         4 . The method of  claim 1 , having a sensitivity of greater than 90%. 
     
     
         5 . The method of  claim 1 , having a specificity of greater than 90%. 
     
     
         6 . The method of  claim 1 , wherein at least one of the at least 32 biomarkers is RNA, cDNA, or protein. 
     
     
         7 . The method of  claim 6 , wherein when the biomarker is RNA, the RNA is reverse transcribed to produce cDNA, and the produced cDNA expression level is detected. 
     
     
         8 . The method of  claim 1 , wherein the expression level of the biomarker is detected by forming a complex between the biomarker and a labeled probe or primer. 
     
     
         9 . The method of  claim 6 , wherein when the biomarker is protein, the protein detected by forming a complex between the protein and a labeled antibody. 
     
     
         10 . The method of  claim 9 , wherein when the label is a fluorescent label. 
     
     
         11 . The method of  claim 6 , wherein when the biomarker is RNA or cDNA, the RNA or cDNA is detected by forming a complex between the RNA or cDNA and a labeled nucleic acid probe or primer. 
     
     
         12 . The method of  claim 11 , wherein the label is a fluorescent label. 
     
     
         13 . The method of  claim 11 , wherein the complex between the RNA or cDNA and the labeled nucleic acid probe or primer is a hybridization complex. 
     
     
         14 . The method of  claim 1 , wherein the test sample is blood, serum, plasma, or a neoplastic tissue. 
     
     
         15 . The method of  claim 1 , wherein the first predetermined cutoff value is derived from a plurality of reference samples obtained from subjects free of a neoplastic disease. 
     
     
         16 . The method of  claim 15 , wherein the reference sample is blood, serum, plasma, or a non-neoplastic tissue. 
     
     
         17 . The method of  claim 1 , further comprising treating the subject identified as having a plasma cell dyscrasia with drug therapy. 
     
     
         18 . The method of  claim 1 , wherein the subject in need thereof is a subject diagnosed with a plasma cell dyscrasia, a subject having at least one plasma cell dyscrasia symptom, or a subject have a predisposition or familial history for developing a plasma cell dyscrasia. 
     
     
         19 . The method of  claim 1 , wherein a subject is human. 
     
     
         20 . The method of  claim 1 , wherein the algorithm is XGB, RF, glmnet, cforest, CART, treebag, knn, nnet, SVM-radial, SVM-linear, NB, NNET, mlp, or logistic regression modelling. 
     
     
         21 . A method for determining whether a plasma cell dyscrasia in a subject is stable or progressive, comprising:
 determining the expression level of at least 32 biomarkers from a test sample from the subject by contacting the test sample with a plurality of agents specific to detect the expression of the at least 32 biomarkers, wherein the at least 32 biomarkers comprise ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2,MALAT1,MBNL1, MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, P1AS2, PRKAA1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, UBE2J1, and at least one housekeeping gene;   normalizing the expression level of each of ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2,MALAT1,MBNL1, MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, PJAS2, PRKAA1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, and UBE2J1 to the expression level of the at least one housekeeping gene, thereby obtaining a normalized expression level of each of ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2,MALAT1, MBNL1, MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, PJAS2, PRKAA1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, and UBE2J1;   inputting each normalized expression level into an algorithm to generate a score;   comparing the score with a second predetermined cutoff value; and   producing a report, wherein the report identifies that the plasma cell dyscrasia is progressive when the score is equal to or greater than the second predetermined cutoff value or identifies that the plasma cell dyscrasia is stable when the score is below the second predetermined cutoff value, wherein the second predetermined cutoff value is 40 on a scale of 0 to 100.   
     
     
         22 . A method for determining a risk of disease relapse in a subject having a plasma cell dyscrasia, comprising:
 determining the expression level of at least 32 biomarkers from a test sample from the subject after treatment by contacting the test sample with a plurality of agents specific to detect the expression of the at least 32 biomarkers, wherein the at least 32 biomarkers comprise ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2, MALAT1, MBNL1, MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, P1AS2, PRKAA 1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, UBE2J1, and at least one housekeeping gene;   normalizing the expression level of each of ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2, MALAT1, MBNL1, MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, P1AS2, PRKAA1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, and UBE2J1 to the expression level of the at least one housekeeping gene, thereby obtaining a normalized expression level of each of ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2, MALAT1, MBNL1, MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, P1AS2, PRKAA1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, and UBE2J1;   inputting each normalized expression level into an algorithm to generate a score;   comparing the score with a third predetermined cutoff value; and   producing a report, wherein the report identifies that the subject has a high risk of disease relapse when the score is equal to or greater than the third predetermined cutoff value or identifies that the subject has a low risk of disease relapse when the score is below the third predetermined cutoff value, wherein the third predetermined cutoff value is 40 on a scale of 0 to 100.   
     
     
         23 . A method for determining a response by a subject having a plasma cell dyscrasia to a therapy, comprising:
 determining a first expression level of at least 31 biomarkers from a first test sample from the subject at a first time point by contacting the first test sample with a plurality of agents specific to detect the expression of the at least 31 biomarkers, wherein the at least 31 biomarkers comprise ASXL1, BHLHE40, BTG2, COPA, FBXW7, GNA13, IL8, JMJD1C, LARS2, MALAT1, MBNL1, MCL1, NFKBIZ (2 splice variants), NR4A1 (2 splice variants), PDE4B, P1AS2, PRKAA1 (2 splice variants), SCYL2 (2 splice variants), SMARCD2, SP1 (2 splice variants), SRSF5, TAGAP, TANK, TLE4, TSC22D3, and UBE2J1;   determining a second expression level of the at least 31 biomarkers from a second test sample from the subject at a second time point by contacting the second test sample with a plurality of agents specific to detect the expression of the at least 31 biomarkers, wherein the second time point is after the first time point and after the administration of the therapy to the subject;   comparing the first expression level with the second expression level; and   producing a report, wherein the report identifies that the subject is responsive to the therapy when the second expression level is significantly decreased as compared to the first expression level.