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

Abstract

Provided herein are methods for diagnosing and treating multiple myeloma based on statistical analysis of and subsequent increasing/inhibiting expression of subgroups of plasma cells and B cell genes. Also provided are methods for a developmental stage-based classification for multiple myeloma using hierarchical clustering analysis of plasma cell and B cell nucleic acids and for discriminating among normal, hyperplastic and malignant using gene expression array data and statistical analysis thereof. In addition methods for determining the risk of developing bone disease in a test individual by examining expression levels of a WNT signaling antagonist, such as DKK1, are provided. A kit comprising anti-DKK1 antibodies and detection reagents for measuring DKK1 protein levels also is provided.

1 . A method of diagnosis for subgroups of multiple myeloma, comprising the steps of:
 isolating plasma cells from an individual; and   examining expression of a group of 24 genes within the plasma cells, said 24 genes having accession numbers X54199, M20902, X89985, M31158, U44111, X16416, HT2811, D16688, U57316, U77456, D13645, M64590, L77701, U20657, L06175, M26311, X04366, AC002115, X06182, M16279, M97676, U10324, S85655, and X63692; and   performing statistical analysis on the expression levels of the genes, wherein a statistically significant value of the analysis provides diagnosis for subgroups of multiple myeloma.   
     
     
         2 . The method of  claim 1 , wherein the expression of the 24 genes is examined at the nucleic acid level or protein level. 
     
     
         3 . A method of treatment for multiple myeloma, comprising:
 inhibiting expression of a gene that has an accession number U09579, U78525, HT5158, X57129, M55210, L77886, U73167, X16416, U57316, Y09022, M25077, AC002115, Y07707, L22005, X66899, D50912, HT4824, U10324, AD000684, U68723, X16323, U24183, D13645, S85655, X73478, L77701, U20657, M59916, D16688, X90392, U07424, X54199, L06175, M55267, M87507, M90356, U35637, L06845, U81001, U76189, U53225, X04366, U77456, L42379, U09578, Z80780, HT4899, M74088, X57985, X79882, X77383, M91592, X63692, M60752, M96684, U16660, M86737, U35113, X81788, HT2217, M62324, U09367, X89985, L19871, X69398, X05323, X04741, D87683, D17525, M64347, U89922, X67325, X59798, U62800, U35340, X12530, X59766, U58096, U52513, X76223, X92689, D17427, L11329, L13210, U10991, L10373, U60873, M65292, HT4215, D13168, AC002077, M92934, X82494, M30703, U9103, or NM012242.   
     
     
         4 . A method of treatment for multiple myeloma, comprising:
 increasing expression of a gene that has an accession number L36033, M63928, U64998, M20902, M26602, M21119, M14636, M26311, M54992, X16832, M12529, M15395, Z74616, HT2152, U97105, U81787, HT3165, M83667, L33930, D83657, M11313, M31158, U24577, M16279, HT2811, M26167, U44111, X59871, X67235, U19713, Y08136, M97676, M64590, M20203, M30257, M93221, S75256, U97188, Z23091, M34344, M25897, M31994, Z31690, S80267, or U00921.   
     
     
         5 . 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 to a DNA microarray;   (d) performing hierarchical clustering analysis on data obtained from the hybridization, wherein the clustering analysis will identify 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; and   (h) performing hierarchical clustering analysis on data obtained from (d) and (g), wherein the clustering analysis classifies the multiple myeloma plasma cells according to the developmental stages of normal B and plasma cells.   
     
     
         6 . The method of  claim 17 , wherein the plasma cells and the B cells individually are isolated from tonsil, bone marrow, mucosal tissue, lymph node, or peripheral blood. 
     
     
         7 . A method of discriminating normal, hyperplastic and malignant plasma cells, comprising the steps of:
 obtaining gene expression data by DNA microarray; and   performing statistical analysis on the data by logistic regression, decision trees, ensembles, naïve bayes, bayesian networks, or support vector machines, wherein the analysis discriminates among normal, hyperplastic and malignant plasma cells.   
     
     
         8 . The method of  claim 7 , wherein altered gene expression discriminates between normal and malignant plasma cells. 
     
     
         9 . A method of determining the risk of developing bone disease in a test individual, comprising:
 examining the expression level of a WNT signaling antagonist in said test individual, wherein increased expression of said antagonist compared to that in normal individual indicates that said test individual has or is at risk for developing bone disease.   
     
     
         10 . The method of  claim 9 , wherein the WNT signaling antagonist is the human homologue of Dickkopf-1 (DKK1) and examining the expression level thereof comprises:
 obtaining biological samples from the test individual; and   examining the level of DKK1 protein in the samples, wherein an increased level of DKK1 protein compared to that in a normal individual indicates that the test individual is at risk of developing bone disease.   
     
     
         11 . The method of  claim 10 , wherein the biological samples are blood samples or bone marrow plasma samples. 
     
     
         12 . The method of  claim 10 , wherein the level of DKK1 protein is determined by an enzyme-linked immunosorbent assay. 
     
     
         13 . The method of  claim 8 , further comprising:
 inhibiting the expression of a WNT signaling antagonist, thereby treating or preventing the bone disease in the individual.   
     
     
         14 . The method of  claim 13 , wherein the expression of said antagonist is inhibited at the nucleic acid level or protein level. 
     
     
         15 . The method of  claim 9 , wherein said WNT signaling antagonist is soluble frizzled related protein 3 (SFRP-3/FRZB) or the human homologue of Dickkopf-1 (DKK1). 
     
     
         16 . The method of  claim 9 , wherein said expression level is determined at the nucleic acid level or protein level. 
     
     
         17 . The method of  claim 9 , wherein said expression level is determined by PCR assays or enzyme-linked immunosorbent assays. 
     
     
         18 . The method of  claim 9 , wherein the test individual has multiple myeloma, osteoporosis, post-menopausal osteoporosis, malignancy-related bone loss, or long term steroid use. 
     
     
         19 . The method of  claim 18 , wherein said malignancy-related bone loss is caused by breast cancer metastasis to the bone or prostate cancer metastasis to the bone. 
     
     
         20 . A kit for measuring the level of DKK1 protein in a biological sample, said kit comprising anti-DKK1 antibodies and reagents for detecting the antibodies.