WO2002031210B1 - Altered hox and wnt7a expression in human lung cancer - Google Patents

Abstract

Alterations in HOX expression have been clearly implicated in leukemia, but their role in most other malignant diseases remains unknown. The present disclosure reports that specific member of the HOX gene family, HOXA9, HOXA10, and HOXB9 are overexpressed in lung cancer cells using are using real-time quantitative assays. In some cases, marked HOX overexpression was associated with elevated FGF10 and 17. During development, the WNT pathway affects cell fate, polarity and proliferation, and WNT7a has been implicated in the maintenance of HOX expression. In contrast to normal lung and mortal short-term bronchial epithelial cultures, WNT7a was frequently reduced or absent in lung cancers. In immortalized bronchial epithelial cells, WNT7a was lost concomitantly with HOXA1, and a statistically significant correlation between the expression of both genes was observed in lung cancer cell lines. Furthermore, we identified a homozygous deletion of β-catenin in the mesothelioma, NCI-H28, associated with reduced WNT7A and the lowest overall cell line expression of HOXA1, A7, A9 and A10 while HOXB9 levels were unaffected. Of note, both WNT7a and beta-catenin are encoded on 3p which undergoes frequent loss in these tumors. Our results indicate that alterations in regulatory circuits involving HOX, WNT, and FGF pathways occur frequently in lung cancer.

Claims

AMENDED CLAIMS

[received by the International Bureau on 18 March 2002 (18.03.02); claim 26 amended; claims 27-30 remain unchanged

(2 pages)]

14. The method of claim 12 wherein the HOX gene is a HOXA gene.

15. The method of claim 14 wherem the HOXA gene includes one or more genes selected from the group consisting of HOXAl, HOXA7, HOXA9 and HOXAIO.

16. The method of claim 12 wherein the desired gene is a HOXB gene.

17. The method of claim 16 wherein the HOXB gene is HOXB9.

18. The method of claim 12 wherein the WNT gene is WNT7a.

19. A method for detecting a gene expression pattern associated with lung cancer comprising the steps of

measuring expression levels of genes selected from the group consisting of HOX and WNT genes in a test cell sample and in a control cell sample of non-malignant lung cells, identifying any of said genes having increased expression or decreased expression in the test cell sample compared to the control cell sample,

Whereby decreased expression of a WNT gene or HOXAl gene, or increased expression of a HOX gene other than HOXAl, or both, is associated with lung cancer.

20. The method of claim 19 wherein the HOX gene is a HOXA or HOXB gene.

21. The method of claim 20 wherein the HOX gene is HOXA.

22. The method of claim 21 wherein HOXA includes one or more genes selected from the group consisting of HOXAl, HOXA7, HOXA9, and HOXAIO.

23. The method of claim 19 wherein the HOX gene is HOXB.

24. The method of claim 23 wherein the HOXB gene is HOXB9.

25. The method of claim 19 wherein the WNT gene is WNT7a.

26. A method for measuring gene expression in a lung cell sample of a lung cancer patient comprising

preparing RNA from the cell sample, amplifying a HOX gene or a WNT gene and a housekeeping gene from the RNA sample by reverse transcriptase polymerase chain reaction (RT-PCR) thereby providing DNA corresponding to the selected gene and the housekeeping gene, measuring the number of rounds of amplification needed to obtain a preset threshold amount of DNA corresponding to the HOX gene or a WNT gene, and of DNA corresponding to the housekeeping gene, 26 normalizing any sample-to-sample variation in the number of rounds of amplification of the HOX gene or a WNT gene to a predetermined number of rounds of amplification of the housekeeping gene needed to obtain the threshold amount of DNA of said housekeeping gene.

27. The method of claim 26 wherein the housekeeping gene is glycerol-3 -phosphate dehydrogenase (G-3-PDH).

28. A method for determining the level of expression of one or more HOX genes in a lung cell sample taken from a patient suspected to have a malignancy compared to the level of expression of said one or more HOX genes in a control sample of non-malignant lung tissue, whereby elevated levels of expression of one or more HOX genes in the sample over the control indicates the presence of malignant cells in the sample.

29. A method for determining the prognosis of a lung cancer by detecting a gene expression pattern associated with lung cancer comprising the steps of

measuring expression levels of genes selected from the group consisting of HOX and WNT genes in a test cell sample and in a control cell sample of non-malignant lung cells,

identifying any of said genes having increased expression or decreased expression in the test cell sample compared to the control cell sample,

whereby decreased expression of a WNT gene or HOXAl gene, or increased expression of a HOX gene other than HOXAl, or both, indicates poor prognosis, increased rate of tumor growth, increased tendency to metastasize.

30. A method for assessing a lung cancer for having a tendency to metastasize by detecting a gene expression pattern associated with lung cancer comprising the steps of

measuring expression levels of genes selected from the group consisting of HOX and WNT genes in a test cell sample and in a control cell sample of non-malignant lung cells,

identifying any of said genes having increased expression or decreased expression in the test cell sample compared to the control cell sample,

whereby decreased expression of a WNT gene or HOXAl gene, or increased expression of a HOX gene other than HOXAl, or both, indicates increased tendency to metastasize.