Diagnosis, prognosis and identification of potential therapeutic targets of multiple myeloma based on gene expression profiling

Abstract

Provided herein is a method for gene expression profiling multiple myeloma patients into distinct subgroups via DNA hybridization and hierarchical clustering analysis of the hybridization data where the results may further be used to identify therapeutic gene targets. Also provided is a method for controlling bone loss in an individual via pharmacological inhibitors of DKK1 protein. In addition provided herein is a method for diagnosing multiple myeloma using a 15-gene model that classifies myeloma into subtypes 1-7.

1 . A method for identifying genes diagnostic of a multiple myeloma in an individual, comprising the steps of:
 isolating plasma cells from individuals with or without multiple myeloma;   obtaining expression profiles of genes comprising the plasma cells isolated from the individuals; and   identifying, via statistical analysis, genes with levels of expression in multiple myeloma patients significantly different from corresponding levels in individuals without multiple myeloma, wherein the genes with a differential expression level are diagnostic of the multiple myeloma in the individual.   
     
     
         2 . The method of  claim 1 , wherein the differentially expressed genes are potential therapeutic targets for multiple myeloma. 
     
     
         3 . The method of  claim 1 , wherein the differentially expressed genes are listed in Table 4, Table 5 and Table 8. 
     
     
         4 . The method of  claim 1 , wherein the differentially expressed genes are GART, APOC1, BCL7B, PRKAR2B, HNMT, ABL1, NEK2, MLLT3, CCN5L2, NAP1L4, KIAA00, GLDC, COX17, USP4, P5-1, S100A9, CAPN1, COX6B, C-KIT, MIC2, MSX1, LIF3, PHB, and DNMT1 and comprise a model to diagnose a subgroup of multiple myeloma. 
     
     
         5 . The method of  claim 1 , wherein the differentially expressed genes are GMPS, CD24, QSCN6, PTPRK, PYGL, PF4V1, ILF3, PLA2G7, MTA1, ABL1, ITGB2, MVP, CD163, and H2B and comprise a model to discriminate among normal, hyperplastic and malignant plasma cells. 
     
     
         6 . The method of  claim 1 , further comprising the step of:
 administering a pharmacological dose of a therapeutic drug or agent effective to alter differential expression of the multiple myeloma genes or to target a biochemical pathway associated with a product of the multiple myeloma genes.   
     
     
         7 . The method of  claim 6 , wherein altering differential gene expression comprises increasing expression of one or more genes in Table 4 or inhibiting expression of one or more of genes in Table 5 and Table 9 or a combination thereof. 
     
     
         8 . A method for diagnosing a subgroup of multiple myeloma in an individual, comprising the steps of:
 isolating plasma cells from an individual; and   obtaining mRNA expression levels of a group of 24 genes GART, APOC1, BCL7B, PRKAR2B, HNMT, ABL1, NEK2, MLLT3, CCN5L2, NAP1L4, KIAA00, GLDC, COX17, USP4, P5-1, S100A9, CAPN1, COX6B, C-KIT, MIC2, MSX1, LIF3, PHB, and DNMT1 in the plasma cells; and   performing statistical analysis on the expression levels of the genes to compute a statistically significant value based on differential expression of the group of genes, wherein the computed value correlates to a diagnosis for a subgroup of multiple myeloma.   
     
     
         9 . The method of  claim 8 , wherein the subgroups of multiple myeloma are MM1, MM2, MM3, and MM4. 
     
     
         10 . A method of discriminating normal, hyperplastic and malignant plasma cells in an individual, comprising the steps of:
 obtaining mRNA expression patterns of a group of fourteen genes GMPS, CD24, QSCN6, PTPRK, PYGL, PF4V1, ILF3, PLA2G7, MTA1, ABL1, ITGB2, MVP, CD163, and H2B in a sample of plasma cells from the individual;   performing a discriminant analysis on the gene expression patterns to compute a discriminant score; and   comparing the discriminant score to a predictive cutoff value statistically determined from a control model of the fourteen genes; wherein a score below the cutoff value is indicative that the plasma cells in the sample are normal and a score above the cutoff is indicative that the plasma cells are hyperplastic or malignant.   
     
     
         11 . A method of developmental stage-based classification for multiple myeloma, comprising the steps of:
 (a) isolating plasma cells and B cells from normal individuals;   (b) isolating nucleic acid samples from the plasma cells and B cells;   (c) hybridizing the nucleic acid samples of (b) to a DNA microarray;   (d) performing hierarchical clustering analysis on data obtained from the hybridization, wherein the clustering analysis identifies differentially expressed genes that classify the plasma cells and B cells according to their developmental stages;   (e) isolating multiple myeloma plasma cells from individuals with multiple myeloma;   (f) isolating nucleic acid samples from the multiple myeloma plasma cells;   (g) hybridizing nucleic acid samples of (f) to a DNA microarray;   (h) performing hierarchical clustering analysis on data obtained from (g); and   (i) comparing the analysis in (h) to that in (d) to classify the multiple myeloma plasma cells according to the developmental stages of normal B and plasma cells.   
     
     
         12 . The method of  claim 11 , wherein the genes differentially expressed during plasma cell differentiation are listed in Table 14. 
     
     
         13 . The method of  claim 11 , wherein the genes differentially expressed during early-stage differentiation of plasma cells are listed in Table 15. 
     
     
         14 . The method of  claim 11 , wherein the genes differentially expressed during late-stage differentiation of plasma cells are listed in Table 16. 
     
     
         15 . The method of  claim 11 , wherein the plasma cells and the B cells individually are isolated from tonsil, bone marrow, mucosal tissue, lymph node, or peripheral blood. 
     
     
         16 . A method for treating a multiple myeloma in an individual, comprising the step of:
 increasing expression of one or more genes in Table 4; or   inhibiting expression of one or more genes in Table 5 and Table 9; or   a combination thereof, thereby altering differential expression of the multiple myeloma genes to treat the individual.