DETECTION OF TISSUE ORIGIN OF CANCER

• US 20100286044A1
• Filed: 12/29/2006
• Published: 11/11/2010
• Est. Priority Date: 12/29/2005
• Status: Abandoned Application

• Current Assignee: Exiqon A/S (Qiagen NV)
• Original Assignee: Exiqon A/S (Qiagen NV)
• Inventors: Møller, Søren, Litman, Thomas, Glue, Christian, Echwald, Søren Morgenthaler, Jacobsen, Nana
• Application Number:
  US11/795,104
• Publication Number:
  US 20100286044A1
• Time in Patent Office: Days
• US Class Current: 514/9.7
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/207 siRNA, miRNA
• CPC Class Codes: C12Q 2527/107 Temperature of melting, i.e. Tm
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/178 miRNA, siRNA or ncRNA

Abstract

Disclosed is a method for determining the cellular or tissue origin of tumor cells. The method entails determining the presence of at least one micro RNA (miRNA) in a sample derived from tumor tissue and based on the said determination establishing a miRNA expression profile and comparing this with pre-established miRNA expression profiles from cells, tissues or tumors. The determination uses short oligonucleotide probes comprising modified affinity-enhancing nucleobases.

Claims

1. A method for specifically identifying, in a mammal, the primary tissue origen of tumor cells in a sample, said method comprising

a) contacting a sample derived from a sample containing tumour cells from with at least one detection probe, which is a member from a collection of detection probes wherein each member of said collection comprises a recognition sequence consisting of nucleobases and affinity enhancing nucleobase analogues, and wherein the recognition sequences exhibit a combination of high melting temperatures and low self-complementarity scores, said melting temperatures being the melting temperature of the duplex between the recognition sequence and its complementary RNA sequence, said collection of detection probes being capable of specifically identifying target RNA sequences in all miRNAs of said mammal and said sample being contacted with said at least one detection probe under conditions that facilitate hybridization between said detection probe and RNA complementary to the recognition sequence of the detection probe, and

b) subsequently detecting hybridization between said at least one detection probe and RNA complementary to the recogntion sequence of the detection probe.

3. The method according to claim 1 or 2, wherein at least 80% of the detection probes in the collection include recognition sequences which exhibit a melting temperature or a measure of melting temperature corresponding to at least 5°

C. higher than a melting temperature or a measure of melting temperature of the self-complementarity score under conditions where the probe hybridizes specifically to its complementary target sequence.

4. The method according to claim 3, wherein at least 90% of the detection probes in the collection include recognition sequences which exhibit a melting temperature or a measure of melting temperature corresponding to at least 5°

C. higher than a melting temperature or a measure of melting temperature of the self-complementarity score under conditions where the probe hybridizes specifically to its complementary target sequence.

5. The method according to claim 3, wherein at least 95% of the detection probes in the collection include recognition sequences which exhibit a melting temperature or a measure of melting temperature corresponding to at least 5°

C. higher than a melting temperature or a measure of melting temperature of the self-complementarity score under conditions where the probe hybridizes specifically to its complementary target sequence.

6. The method according to claim 3, wherein all of the detection probes in the collection include recognition sequences which exhibit a melting temperature or a measure of melting temperature corresponding to at least 5°

C. higher than a melting temperature or a measure of melting temperature of the self-complementarity score under conditions where the probe hybridizes specifically to its complementary target sequence.

7. The method according to any one of the preceding claims, wherein the melting temperature or the measure of melting temperature is at least 10°

C., such as at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, and at least 50°

C. higher than a melting temperature or measure of melting temperature of the self-complementarity score.

8. The method according to any one of the preceding claims, wherein the collection comprises at least 10 detection probes, 15 detection probes, such as at least 20, at least 25, at least 50, at least 75, at least 100, at least 200, at least 500, at least 1000, and at least 2000 members.

9. The method according to any one of the preceding claims, wherein the miRNA is mature miRNA.

10. The method according to any one of the preceding claims, wherein the mammal is a human being.

11. The method according to any one of the preceding claims, wherein the affinity-enhancing nucleobase analogues are regularly spaced between the nucleobases in at least 80% of the members of said collection, such as in at least 90% or at least 95% of said collection.

12. The method according to any one of the preceding claims, wherein the 3′

and 5′

nucleobases are not substituted by affinity enhancing nucleobase analogues.

13. The method according to any one of the preceding claims, wherein the presence of the affinity enhancing nucleobases in the recognition sequence confers an increase in the binding affinity between a detection probe and its complementary target RNA sequence relative to the binding affinity exhibited by a corresponding probe, which only include nucleobases.

14. The method according to any one of the preceding claims, wherein the affinity enhancing nucleobase analogues are LNA nucleobases.

15. The method according to any one of the preceding claims, wherein the affinity enhancing nucleobase analogues are regularly spaced as every 2^nd, every 3^rd, every 4^th or every 5^th nucleobase in the recognition sequence, preferably as every 3^rd nucleobase.

16. The method according to any one of the preceding claims, wherein the recognition sequence is at least a 6-mer, such as at least a 7-mer, at least an 8-mer, at least a 9-mer, at least a 10-mer, at least an 11-mer, at least a 12-mer, at least a 13-mer, at least a 14-mer, at least a 15-mer, at least a 16-mer, at least a 17-mer, at least an 18-mer, at least a 19-mer, at least a 20-mer, at least a 21-mer, at least a 22-mer, at least a 23-mer, and at least a 24-mer.

17. The method according to any one of claims 1-15, wherein the recognition sequence is at most a 25-mer, such as at most a 24-mer, at most a 23-mer, at most a 22-mer, at most a 21-mer, at most a 20-mer, at most a 19-mer, at most an 18-mer, at most a 17-mer, at most a 16-mer, at most a 15-mer, at most a 14-mer, at most a 13-mer, at most a 12-mer, at most an 11-mer, at most a 10-mer, at most a 9-mer, at most an 8-mer, at most a 7-mer, and at most a 6-mer.

18. The method according to any one of the preceding claims, wherein at least 80% of the detection probes comprise recognition sequences of the same length, such as at least 90% or at least 95%.

19. The method according to claim 18, wherein all detection probes contain affinity enhancing nucleobase analogues with the same regular spacing in the recognition sequences.

20. The method according to any one of the preceding claims, wherein at least one of the nucleobases in the recognition sequence is substituted with its corresponding selectively binding complementary (SBC) nucleobase.

21. The method according to any one of the preceding claims, wherein the nucleobases in the sequence are selected from ribonucleotides and deoxyribonucleotides.

22. The method according to claim 21, wherein the recognition sequence consists of affinity enhancing nucleobase analogues together with either ribonucleotides or deoxyribonucleotides.

23. The method according to any one of the preceding claims, wherein each detection probe is covalently bonded to a solid support.

24. The method according to claim 23, wherein the solid support is selected from a bead, a microarray, a chip, a strip, a chromatographic matrix, a microtiter plate, and a fiber.

25. The method according to any one of the preceding claims, wherein each detection probe includes a detection moiety and/or a ligand, optionally in the recognition sequence.

26. The method according to any one of the preceding claims, wherein each detection probe includes a photochemically active group, a thermochemically active group, a chelating group, a reporter group, or a ligand that facilitates the direct of indirect detection of the probe or the immobilisation of the probe onto a solid support.

27. The method according to any one of the preceding claims, wherein the detection probe includes a recognition sequence selected from the LNA containing recognition sequences set forth in table U and/or includes a recognition sequence capable of binding specifically to a miRNA set forth in Table T.

28. The method according to claim any one of the preceding claims, wherein at least one miRNA species is detected in the sample comprising RNA from the sample comprising tumour cells, thus providing a miRNA expression profile from the tumour, and subsequently comparing said miRNA expression profile with previously established miRNA expression profiles from normal tissue and/or tumour tissue.

29. The method according to claim any one of the preceding claims, wherein the sample is total RNA from the sample containing tumour cells.

30. The method according to claim 28 or 29, wherein comparison between the miRNA expression profile from the tumour and the previously established miRNA expression profiles provides for an indication of the origin of the tumour, the patient'"'"'s prognosis, the optimum treatment regimen of the tumour and/or a prediction of the outcome of a given anti-tumour treatment.

31. The method according to any one of the preceding claims, wherein the miRNA has a length of at most 30 residues, such as at most 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, or 18 residues.

32. The method according to any one of claims 1-30, wherein the miRNA has a length of at least 15 residues, such as at least 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 residues.

33. The method according to any one of the preceding claims, wherein the miRNA is present in a fixated, embedded sample such as a formalin fixated paraffin embedded sample.

34. The method according to any one of the preceding claims, which is used in diagnosis, prognosis, therapy outcome prediction, and therapy.

35. The method according to any one of the preceding claims, wherein the tumour of unknown origin is compared to an expression pattern characteristic of a) tumours derived lymph nodes and tonsils, b) tumours derived from tongue and throat and c) tumours derived from the esophagus.

36. The method according to any one of the preceding claims, wherein the metastatic tumour is a carcinoma.

2. A method for specifically identifying, in a mammal, the tissue of origin of a tumour of unknown origin, said method comprising

a) contacting a sample derived from a sample containing tumour cells of said tumour with at least one detection probe, which is a member from a collection of detection probes wherein each member of said collection comprises a recognition sequence consisting of nucleobases and affinity enhancing nucleobase analogues, and wherein the recognition sequences exhibit a combination of high melting temperatures and low self-complementarity scores, said melting temperatures being the melting temperature of the duplex between the recognition sequence and its complementary RNA sequence, said collection of detection probes being capable of specifically identifying target RNA sequences in all miRNAs of said mammal and said sample being contacted with said at least one detection probe under conditions that facilitate hybridization between said detection probe and RNA complementary to the recognition sequence of the detection probe, and

b) subsequently detecting hybridization between said at least one detection probe the RNA complementary complementary to the detection probe.

37. A method of for the treatment of cancer, said method comprising

a. isolating RNA from at least one tissue sample from a patient suffering from cancer,

b. establishing an miRNA expression profile utilising RNA isolated in step a and determining at least one feature of said cancer which conforms with the miRNA expression profile,

c. based on the identification feature determined in step b) diagnosing the physiological status of the cancer disease in said patient, and

d. selecting and applying an appropriate form of therapy for said patient based on the said diagnosis.

38. The method according to claim 37, wherein the at least one feature of said cancer is selected from one or more of the group consisting of:

presence or absence of said cancer;

type of said cancer;

origin of said cancer;

diagnosis of cancer;

prognosis of said cancer;

therapy outcome prediction;

therapy outcome monitoring;

suitability of said cancer to treatment, such as suitability of said cancer to chemotherapy treatment and/or radiotherapy treatment;

suitability of said cancer to hormone treatment;

suitability of said cancer for removal by invasive surgery;

suitability of said cancer to combined adjuvant therapy.

39. The method of for the treatment of cancer according to claim 38, wherein the at least one feature of said cancer is determination of the origin of said cancer, wherein said cancer is a metestasis and/or a secondary cancer which is remote from the cancer of origin, such as the primary cancer.

40. The method for the treatment of cancer according to claim 38 or 39, wherein the treatment comprises one or more of the therapies selected from the group consisting of:

chemotherapy;

hormone treatment;

invasive surgery;

radiotherapy; and

adjuvant systemic therapy.