Genes associate with progression and response in chronic myeloid leukemia and uses thereof

• US 20070154931A1
• Filed: 12/14/2006
• Published: 07/05/2007
• Est. Priority Date: 12/15/2005
• Status: Active Grant

• Current Assignee: Fred Hutchinson Cancer Research Center (Fred Hutchinson Cancer Research Center|Argus Genetics|Mars), Rosetta Inpharmatics LLC (Merck & Co., Inc.)
• Original Assignee: Fred Hutchinson Cancer Research Center (Fred Hutchinson Cancer Research Center|Argus Genetics|Mars)
• Inventors: Mao, Mao, Linsley, Peter, Dai, Hongyue, Schelter, Janell, Radich, Jerald
• Granted Patent: US 8,014,957 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• 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

The invention provides molecular markers that are associated with the progression of chronic myeloid leukemia (CML), and methods and computer systems for monitoring the progression of CML in a patient based on measurements of these molecular markers. The present invention also provides CML target genes, and methods and compositions for treating CML patients by modulating the expression or activity of these CML target genes and/or their encoded proteins. The invention also provides genes that are associated with resistance to imatinib mesylate (Gleevec™) treatment in CML patients, and methods and compositions for determining the responsiveness of a CML patient to imatinib mesylate treatment based on measurements of these genes and/or their encoded proteins. The invention also provides methods and compositions for enhancing the effect of Gleevec™ by modulating the expression or activity of these genes and/or their encoded proteins.

Claims

1. A method for determining the progression of chronic myeloid leukemia (CML) in a patient, comprising

(a) classifying a marker profile comprising measurements of a plurality of gene products in a cell sample taken from said patient as a chronic phase (CP-CML) profile or as an advanced phase (ADV-CML) profile, wherein said gene products are respectively products of at least 5 of the genes listed in Table 1a and/or Table 1b or respective functional equivalents thereof, wherein at least one of said at least 5 genes is from Table 1a;

and

(b) determining said patient as in a chronic phase if said marker profile is classified as a CP-CML profile, or determining said patient as in an advanced phase if said marker profile is classified as an ADV-CML profile.

2. The method of claim 1, wherein said plurality of gene products are of at least 5 of the genes listed in Table 1a.

3. The method of claim 1, further comprising obtaining said marker profile by a method comprising measuring said plurality of gene products in a cell sample taken from said patient.

4. The method of claim 3, wherein said cell sample is a sample selected from the group consisting of bone marrow sample and peripheral blood sample.

5. The method of claim 1, wherein said classifying is carried out using a progression classifier, wherein said progression classifier receives an input comprising said marker profile and provides an output comprising data indicating whether said marker profile is a CP-CML profile or an ADV-CML profile.

6. The method of claim 5, wherein said progression classifier comprises a CP-CML template comprising measurements of said plurality of gene products representative of measurements of said plurality of genes products in a plurality of patients having CP-CML and/or an ADV-CML template comprising measurements of said plurality of gene products representative of measurements of said plurality of genes products in a plurality of patients having ADV-CML, wherein said step of classifying is carried out by a method comprising (i) comparing said marker profile with said CP-CML template and/or said ADV-CML template;

and (ii) classifying said marker profile as a CP-CML profile if said marker profile has a high similarity to said CP-CML template and/or has a low similarity to said ADV-CML template, or classifying said marker profile as a ADV-CML profile if said marker profile has a high similarity to said ADV-CML template and/or has a low similarity to said CP-CML template, wherein a high similarity corresponds to a degree of similarity above a predetermined threshold, and wherein a low similarity corresponds to a degree of similarity no greater than said predetermined threshold.

7. The method of claim 6, wherein said step of classifying is carried out by a method comprising (i) comparing said marker profile with said CP-CML template or said ADV-CML template;

and (ii) classifying said marker profile as a CP-CML profile if said marker profile has a high similarity to said CP-CML template or has a low similarity to said ADV-CML template, or classifying said marker profile as a ADV-CML profile if said marker profile has a high similarity to said ADV-CML template or has a low similarity to said CP-CML template, wherein a high similarity corresponds to a degree of similarity above a predetermined threshold, and wherein a low similarity corresponds to a degree of similarity no greater than said predetermined threshold.

8. The method of claim 6, wherein said step of classifying is carried out by a method comprising (i) comparing said marker profile with said CP-CML template and said ADV-CML template;

and (ii) classifying said marker profile as a CP-CML profile if said marker profile has a higher similarity to said CP-CML template than to said ADV-CML template, or classifying said marker profile as a ADV-CML profile if said marker profile has a higher similarity to said ADV-CML Ltmplate than to said CP-CML template.

9. The method of claim 5, wherein said progression classifier is an artificial neural network (ANN) or a support vector machine (SVM).

10. The method of claim 1, wherein said gene products are products of at least 10 of the genes listed in Table 1a and/or 1b.

11. The method of claim 1, wherein said gene products are products of at least 10 of the genes listed in Table 2a.

12. The method of claim 1, wherein said gene products are products of at least 5 of the genes corresponding to the markers listed in Table 3.

13. The method of claim 12, wherein said gene products are products of at least 5 of the genes corresponding to the up-regulated markers listed in Table 3, or are products of at least 5 of the genes corresponding to the down-regulated markers listed in Table 3.

14. The method of claim 1, wherein each of said gene products is a gene transcript.

15. The method of claim 14, wherein measurement of each said gene transcript is obtained by a method comprising contacting a positionally-addressable microarray with nucleic acids from said cell sample or nucleic acids derived therefrom under hybridization conditions, and detecting the amount of hybridization that occurs, said microarray comprising one or more polynucleotide probes complementary to a hybridizable sequence of each said gene transcript.

16. The method of claim 14, wherein measurement of each said gene transcript is obtained by quantitative reverse transcriptase PCR (qRT-PCT).

17. The method of claim 1, wherein each of said plurality of gene products is a protein.

18. A method for determining the responsiveness of a chronic myeloid leukemia (CML) patient to imatinib mesylate (IM), comprising (a) determining the progression of said patient using a method as claimed in claim 1;

and (b) determining said patient as responsive to IM treatment if said marker profile is classified as a CP-CML profile, or determining said patient as resistant to IM treatment if said marker profile is classified as an ADV-CML profile.

19. A method for determining the responsiveness of a chronic myeloid leukemia (CML) patient to imatinib mesylate (IM), comprising

(a) classifying a marker profile comprising measurements of a plurality of gene products in a cell sample taken from said patient as an IM-sensitive profile or an IM-resistant profile, wherein said gene products are respectively products of at least 5 of the genes listed in Table 4 or respective functional equivalents thereof;

and

(b) determining said patient as responsive to IM treatment if said marker profile is classified as an IM-sensitive profile, or determining said patient as resistant to IM treatment if said marker profile is classified as an IM-resistant profile.

20. The method of claim 19, further comprising obtaining said marker profile by a method comprising measuring said plurality of gene products in a cell sample taken from said patient.

21. The method of claim 20, wherein said cell sample is a sample selected from the group consisting of bone marrow sample and peripheral blood sample.

22. The method of claim 19, wherein said classifying is carried out by a method comprising using a progression classifier, wherein said progression classifier receives an input comprising said marker profile and provides an output comprising data indicating whether said marker profile is an IM-sensitive profile or an IM-resistant profile.

23. A method for identifying a set of genes that are associated with progression of chronic myeloid leukemia (CML), comprising:

(a) subtracting from each of a plurality of CML expression profiles a CD34+ expression profile to obtain a plurality of CD34+(−

) CML expression profiles, each said CML expression profile comprising levels of expression of a plurality of genes in cells of one of a plurality of chronic myeloid leukemia (CML) patients, said CD34+ expression profile comprising levels of expression of said plurality of genes in non cancerous immature CD34+ cells, said plurality of CML patients comprising patients of different phases of CML; and

(b) comparing said plurality of CD34+(−

) CML expression profiles; and

(c) identifying one or more genes that exhibit significant differences in levels of expression between different phases of CML across said plurality of CD34+(−

) CML expression profiles.

24. The method of claim 23, wherein said comparing is carried out by ANOVA and wherein said identifying is carried out by identifying one or more genes one or more genes whose p-value corresponds to a predetermined significance level.

25. The method of claim 24, wherein said predetermined significance level is p<

10<sup>−

8</sup>.

26. The method of claim 23, further comprising:

(d) comparing levels of expression of said identified genes between cells of CML blast crisis and normal immature CD34+ cells; and

(e) selecting those genes that exhibit significant differences in expression.

27. The method of claim 26, wherein said comparing is carried out by ANOVA and wherein said selecting is carried out by selecting one or more genes whose p-value corresponds to a predetermined significance level.

28. The method of claim 27, where said predetermined significance level is p-value <

0.01%.