TP53 gene expression and uses thereof

• US 20080234138A1
• Filed: 12/07/2007
• Published: 09/25/2008
• Est. Priority Date: 12/08/2006
• Status: Abandoned Application

• Current Assignee: The Board of Trustees of the University of Arkansas (University of Arkansas System)
• Original Assignee: The Board of Trustees of the University of Arkansas (University of Arkansas System)
• Inventors: Barlogie, Bart, Shaughnessy, John D.
• Application Number:
  US11/999,766
• Publication Number:
  US 20080234138A1
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/178 miRNA, siRNA or ncRNA

Abstract

The present invention is drawn to diagnosis, prognosis and treatment of multiple myeloma. In this regard, the present invention discloses importance of down-regulation of TP3 gene in multiple myeloma and its use as an independent progostic indicator of multiple myeloma. Additionally, the present invention also discloses novel-TP53 associated genes and demonstrates the clinical relevance of these alterations to disease progression.

Claims

1. A method for identifying a gene as an independent prognostic factor specific for a disease, comprising:

isolating plasma cells from individuals within a population;

extracting nucleic acid from said plasma cells;

hybridizing said nucleic acid to a DNA array to determine expression levels of genes in the plasma cells; and

performing multivariate regression analyses on data obtained from said hybridization, wherein said analysis identifies the gene as an independent prognostic factor specific for a disease.

2. The method of claim 1, wherein the low expression of said gene correlates with poor prognosis, deletion in chromosome, decreased gene copy number or a combination thereof.

3. The method of claim 2, wherein said prognosis comprises a shorter event-free and overall survival.

4. The method of claim 2, wherein the deletion is on chromosome 17p13.

5. The method of claim 1, wherein the gene identified as an independent prognostic factor specific for a disease is TP53, wherein said disease is cancer.

10. The method of claim 1, further comprising:

performing gene expression profiling to identify genes associated with the gene linked to survival specific for the disease.

11. The method of claim 1, wherein said genes are selected from the group consisting of TRIM13, NADSYN1, TRIM22, AGRN, CENTD2, SESN1, TM7SF2, NICKAP1, COPG, STAT3, ALOX5, APP, ABCB9, GAA, CEP55, BRCA1, ANLN, PYGL, CCNE2, ASPM, SUV39H2, CDC25A, IFIT5, ANKRA2, PHLDB1, TUBA1A, CDCA7, CDCA2, HFE, RIF1, NEIL3, SLC4A7, FXYD5, MCC, MKNK2, KLHL24, DLC1, OPN3, B3GALNT1, SPRED1, ARHGAP25, RTN2, WNT16, DEPDC1, STT3B, ECHDC2, ENPP4, SAT2, SLAMF7, MAN1C1, INTS7, ZNF600, L3MBTL4, LAPTM4B, OSBPL10, KCNS3, THEX1. CYB5D2, UNC93B1, SIDT1, TMEM57, HIGD24, FKSG44, C14orf28, LOC387763, TncRNA, C18orf1, DCUN1D4, FANCI, ZMAT3, NOTCH1, BTG2, RAB1A, TNFRSF10B, HDLBP, RIT1, KIF2C, S100A4, MEIS1, SGOL2, CD302, C5orf34, FAM111B and C18orf54.

12. The method of claim 1, wherein said method correlates the expression of the gene to survival of an individual suffering from the disease, with molecular classification of the disease, with molecular risk stratification of the disease to predict outcome or a combination thereof.

13. The method of claim 12, wherein low expression of said gene correlates with the high-risk molecular classification of the disease.

14. The method of claim 13, wherein the high-risk molecular classification of multiple myeloma is characterized by increased combined expression of MMSET, MAF/MAFB and PROLIFERATION signatures.

19. The method of claim 1, wherein the individual with poor prognosis has up-regulated expression of one or more genes selected from the group consisting of CEP55, BRCA1, ANLN, PYGL, CCNE2, ASPM, SUV39H2, CDC25A, TUBA1A, CDCA7, CDCA2, HFE, RIF1, NEIL3, SLC4A7, OPN3, B3GALNT1, SPRED1, DEPDC1, ENPP4, INTS7, L3MBTL4, THEX1, DCUN1D4, FANCI, ZMAT3, NOTCH1, BTG2, RAB1A, TNFRSF10B, HDLBP, RIT1, KIF2C, S100A4, MEIS1, SGOL2, CD302, C5orf34, FAM111B and C18orf54;

and has down-regulated expression of TP53 alone or in combination with one or more genes selected from the group consisting of TRIM13, NADSYN1, TRIM22, AGRN, CENTD2, SESN1, TM7SF2, NICKAP1, COPG, STAT3, ALOX5, APP, ABCB9, GAA, IFIT5, ANKRA2, PHLDB1, FXYD5, MCC, MKNK2, KLHL24, DLC1, ARHGAP25, RTN2, WNT16, STT3B, ECHDC2, SAT2, SLAMF7, MAN1C1, ZNF600, LAPTM4B, OSBPL10, KCNS3, CYB5D2, UNC93B1, SIDT1, TMEM57, HIGD24, FKSG44, C14orf28, LOC387763, TncRNA and C18orf1.

20. The method of claim 1, wherein the poor prognosis comprises a shorter event-free and overall survival, a high-risk subtype of the multiple myeloma or both.

21. The method of claim 20, wherein the high-risk subtype of multiple myeloma is further characterized by increased combined expression of MMSET, MAF/MAFB and PROLIFERATION signatures.

6. The method of claim 6, wherein the cancer is multiple myeloma.

7. A method for identifying a gene relevant in prognosis of a disease, comprising:

isolating plasma cells from individuals within a population;

extracting nucleic acid from said plasma cells;

hybridizing said nucleic acid to a DNA microarray; and

performing log rank test on the data obtained from said hybridization to identify genes that are up-regulated and down-regulated in the plasma, thereby identifying the gene important for prognosis of the disease.

8. The method of claim 7, further comprising:

analyzing nucleic acid obtained from the plasma cells; and

performing log rank test on data obtained after analyzing the nucleic acid, wherein said test correlates the status of the gene with progression and outcome of the disease.

9. The method of claim 8, wherein said analysis of the nucleic acid comprises determining mRNA expression of the gene, sequence integrity of the gene, copy number of the gene or a combination thereof.

15. The method of claim 7, wherein said prognosis comprises a shorter event-free and overall survival.

16. The method of claim 7, wherein the gene is TP53 and the disease is cancer.

17. The method of claim 16, wherein the cancer is multiple myeloma.

18. A method for determining prognosis of an individual with multiple myeloma, comprising:

obtaining plasma cells from the individual; and

determining expression of TP53 alone or in combination with one or more genes selected from the group consisting of TRIM13, NADSYN1, TRIM22, AGRN, CENTD2, SESN1, TM7SF2, NICKAP1, COPG, STAT3, ALOX5, APP, ABCB9, GAA, CEP55, BRCA1, ANLN, PYGL, CCNE2, ASPM, SUV39H2, CDC25A, IFIT5, ANKRA2, PHLDB1, TUBA1A, CDCA7, CDCA2, HFE, RIF1, NEIL3, SLC4A7, FXYD5, MCC, MKNK2, KLHL24, DLC1, OPN3, B3GALNT1, SPRED1, ARHGAP25, RTN2, WNT16, DEPDC1, STT3B, ECHDC2, ENPP4, SAT2, SLAMF7, MAN1C1, INTS7, ZNF600, L3MBTL4, LAPTM4B, OSBPL10, KCNS3, THEX1. CYB5D2, UNC93B1, SIDT1, TMEM57, HIGD24, FKSG44, C14orf28, LOC387763, TncRNA, C18orf1, DCUN1D4, FANCI, ZMAT3, NOTCH1, BTG2, RAB1A, TNFRSF10B, HDLBP, RIT1, KIF2C, S100A4, MEIS1, SGOL2, CD302, C5orf34, FAM111B and C18orf54; and

comparing the expression level of the gene(s) with expression level of the gene in a control individual such that genes that are up-regulated, down-regulated or a combination thereof compared to gene expression levels in plasma cell of a control individual indicates prognosis of said individual.

22. The method of claim 18, wherein the gene expression is determined by RT-PCR or DNA microarray.

23. The method of claim 18, wherein said control individual is a normal healthy individual.

24. A kit for prognosis of multiple myeloma, comprising:

nucleic acid probes complementary to mRNA of genes described in claim 18; and

written instructions for extracting nucleic acid from plasma cells of an individual and hybridizing said nucleic acid to the DNA microarray.