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

• US 20040009523A1
• Filed: 06/04/2003
• Published: 01/15/2004
• Est. Priority Date: 11/07/2001
• Status: Active Grant

• Current Assignee: Bioventures, LLC
• Original Assignee: The Board of Trustees of the University of Arkansas (University of Arkansas System)
• Inventors: Zhan, Fenghuang, Barlogie, Bart, Shaughnessy, John D.
• Granted Patent: US 7,308,364 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

Gene expression profiling between normal B cells/plasma cells and multiple myeloma cells revealed four distinct subgroups of multiple myeloma plasma cells that have significant correlation with clinical characteristics known to be associated with poor prognosis. Diagnosis for multiple myeloma (and possibly monoclonal gammopathy of undetermined significance) based on differential expression of 14 genes, as well as prognostics for the four subgroups of multiple myeloma based on the expression of 24 genes were also established. Gene expression profiling also allows placing multiple myeloma into a developmental schema parallel to that of normal plasma cell differentiation. The development of a gene expression- or developmental stage-based classification system for multiple myeloma would lead to rational design of more accurate and sensitive diagnostics, prognostics and tumor-specific therapies for multiple myeloma.

Claims

1. A method of gene expression profiling for multiple myeloma, comprising the steps of:

isolating plasma cells from individuals with or without multiple myeloma;

isolating nucleic acid samples from said plasma cells;

hybridizing said nucleic acid samples to a DNA microarray; and

performing hierarchical clustering analysis on data obtained from said hybridization, wherein said clustering analysis will classify said individuals with or without multiple myeloma into distinct subgroups.

2. The method of claim 1, wherein said subgroups of multiple myeloma are MM1, MM2, MM3 and MM4.

3. The method of claim 1, wherein said clustering analysis will identify genes with elevated expression in subsets of multiple myeloma patients.

4. The method of claim 3, wherein said genes have accession number selected from the group consisting of M64347, U89922, X67325, X59798, U62800, U35340, X12530, X59766, U58096, U52513, X76223, X92689, D17427, L11329, L13210, U10991, L10373, U60873, M65292, HT4215, D13168, AC002077, M92934, X82494, and M30703.

5. The method of claim 1, wherein said clustering analysis will identify genes with significantly different levels of expression in multiple myeloma patients as compared to normal individuals, wherein said genes are potential therapeutic targets for multiple myeloma.

6. The method of claim 5, wherein said potential therapeutic targets for multiple myeloma are genes that have accession number selected from the group consisting of 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, U00921, 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 and NM012242.

7. A method of identifying a group of genes that can distinguish between normal plasma cells and plasma cells of multiple myeloma, comprising the steps of:

isolating plasma cells from individuals with or without multiple myeloma;

isolating nucleic acid samples from said plasma cells;

hybridizing said nucleic acid samples to a DNA microarray;

identifying differential gene expression patterns that are statistically significant; and

applying linear regression analysis to identify a group of genes, wherein said group of genes is capable of accurate discrimination between normal plasma cells and plasma cells of multiple myeloma.

8. The method of claim 7, wherein said genes have accession number HT5158, L33930, L42379, L77886, M14636, M26167, U10324, U24577, U35113, X16416, X64072, X79882, Z22970, and Z80780.

9. The method of claim 7, wherein said group of genes is capable of accurate discrimination between subgroups of multiple myeloma.

10. The method of claim 9, wherein said genes have accession number 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.

11. A method of diagnosis for multiple myeloma, comprising the steps of:

isolating plasma cells from an individual;

examining expression of a group of 14 genes within said plasma cells, said 14 genes have accession numbers HT5158, L33930, L42379, L77886, M14636, M26167, U10324, U24577, U35113, X16416, X64072, X79882, Z22970, and Z80780; and

performing statistical analysis on the expression levels of said genes, wherein a statistically significant value of said analysis indicates that said individual has multiple myeloma.

12. The method of claim 11, wherein the expression of said 14 genes is examined at the nucleic acid level or protein level.

13. A method of diagnosis for subgroups of multiple myeloma, comprising the steps of:

isolating plasma cells from an individual;

examining expression of a group of 24 genes within said plasma cells, said 24 genes have 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 said genes, wherein a statistically significant value of said analysis provides diagnosis for subgroups of multiple myeloma.

14. The method of claim 13, wherein the expression of said 24 genes is examined at the nucleic acid level or protein level.

15. A method of treatment for multiple myeloma, comprising the step of:

inhibiting expression of a gene that has accession number selected from the group consisting of 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 and NM012242.

16. A method of treatment for multiple myeloma, comprising the step of:

increasing expression of a gene that has accession number selected from the group consisting of 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, U00921.

17. 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 said plasma cells and B cells;

(c) hybridizing said nucleic acid samples to a DNA microarray;

(d) performing hierarchical clustering analysis on data obtained from said hybridization, wherein said clustering analysis will identify genes that classify said 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 said multiple myeloma plasma cells;

(g) hybridizing nucleic acid samples of (f) to a DNA microarray;

(h) performing hierarchical clustering analysis on data obtained from (d) and (g), wherein said clustering analysis will classify said multiple myeloma plasma cells according to the developmental stages of normal B and plasma cells.

18. The method of claim 17, wherein said plasma cells are isolated from an organ selected from the group consisting of tonsil, bone marrow, mucoal tissue, lymph node and peripheral blood.

19. The method of claim 17, wherein said B cells are isolated from an organ selected from the group consisting of tonsil, bone marrow, lymph node and peripheral blood.

20. 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 said data by a method selected from the group consisting of logistic regression, decision trees, ensembles, naive bayes, bayesian networks and support vector machines, wherein said analysis would discriminate among normal, hyperplastic and malignant plasma cells.

21. The method of claim 20, wherein said analysis would identify a gene with altered expression between normal and malignant plasma cells.

22. A method of controlling bone loss in an individual, comprising the step of inhibiting the expression of the DKK1 gene (accession number NM012242) or the activity of the protein expressed by the DKK1 gene.

23. The method of claim 22, wherein said DKK1 gene expression is inhibited by anti-sense oligonucleotides or by anti-DKK1 antibodies.

24. A method of controlling bone loss in an individual, comprising the step of administering to said individual a pharmacological inhibitor of DKK1 protein.

25. The method of claim 24, wherein said individual has a disease selected from the group consisting of multiple myeloma, osteoporosis, post-menopausal osteoporosis and malignancy-related bone loss.

26. The method of claim 25, wherein said malignancy-related bone loss is caused by breast cancer metastasis to the bone or prostate cancer metastasis to the bone.