# Patent

## Title
Use of VEGFR1 as a biomarker

## Abstract

The present invention is related to the use of VEGFR1 or of a nucleic acid coding for VEGFR1 as a biomarker in a method for the treatment of a subject, wherein the method for the treatment comprises administering to the subject a PKN3 inhibitor.

## Background
The Sequence Listing for this application is labeled “29V9763.TXT” which was created on Jul. 19, 2013 and is 71 KB. The entire contents of the sequence listing is incorporated herein by reference in its entirety.
The present invention is related to the use of vascular endothelial growth factor receptor 1 (VEGFR1) or of a nucleic acid coding for VEGFR1 as a biomarker, a method for deciding whether a subject is a responder to a method of treatment, a method for deciding whether a subject having undergone a first method of treatment, wherein the first method of treatment comprises administering to the subject a PKN3 inhibitor, shall be subject to a second method of treatment, wherein the second method of treatment comprises administering to the subject a PKN3 inhibitor, a method for deciding whether a subject shall undergo a method of treatment, whereby the method of treatment comprises the administration of a PKN3 inhibitor, and a PKN3 inhibitor for use in a method for the treatment of a subject suffering from or being at risk of suffering from a disease.
Oncogenesis was described by Foulds (Foulds, L. (1958), J Chronic Dis, 8, 2-37) as a multistep biological process, which is presently known to occur by the accumulation of genetic damage. On a molecular level, the multistep process of tumorigenesis involves the disruption of both positive and negative regulatory effectors (Weinberg, R. A. (1989); Cancer Res, 49, 3713-3721). The molecular basis for human colon carcinomas has been postulated, by Vogelstein and coworkers (Fearon, E. R. and Vogelstein, B. (1990), Cell, 61, 759-767), to involve a number of oncogenes, tumor suppressor genes and repair genes. Similarly, defects leading to the development of retinoblastoma have been linked to another tumor suppressor gene (Lee, W. H., et al. (1987) Science, 235, 1394-1399). Still other oncogenes and tumor suppressors have been identified in a variety of other malignancies. Unfortunately, there remains an inadequate number of treatable cancers, and the effects of cancer are catastrophic—over half a million deaths per year in the United States alone.
Cancer is fundamentally a genetic disease in which damage to cellular DNA leads to disruption of the normal mechanisms that control cellular proliferation. Two of the mechanisms of action by which tumor suppressors maintain genomic integrity is by cell arrest, thereby allowing for repair of damaged DNA, or removal of the damaged DNA by apoptosis (Ellisen, L. W. and Haber, D. A. (1998), Annu Rev Med, 49, 425-436). Apoptosis, otherwise called “programmed cell death,” is a carefully regulated network of biochemical events which act as a cellular suicide program aimed at removing irreversibly damaged cells. Apoptosis can be triggered in a number of ways including binding of tumor necrosis factor, DNA damage, withdrawal of growth factors, and antibody cross-linking of Fas receptors. Although several genes have been identified that play a role in the apoptotic process, the pathways leading to apoptosis have not been fully elucidated. Many investigators have attempted to identify novel apoptosis-promoting genes with the objective that such genes would afford a means to induce apoptosis selectively in neoplastic cells to treat lancer in a patient.
An alternative approach to treating cancer involves the suppression of angiogenesis with an agent such as EndostatinTM or anti-VEGF antibodies. In this approach, the objective is to prevent further vascularization of the primary tumor and potentially to constrain the size of metastatic lesions to that which can support neoplastic cell survival without substantial vascular growth.
A particular group of cancer diseases are those cancer diseases which are aggressive in terms of growth rate of the tumor, invasion into normal tissue, resistance to chemotherapy or other conventional treatments and the formation of metastasis throughout the body. In the case of more aggressive cancer, the cancer tissue is more different from the normal tissue and the tumor is more likely to spread. Therefore one objective in current cancer research is to develop agents which are inhibiting tumor growth and/or reducing the spreading of cancer cells throughout the body.
Definitions for what is an aggressive cancer disease may be taken from the homepage of the National Cancer Institute which is Worldwide Website: cancer.gov/Templates/db_alpha.aspx?CdrID=46053. Also, for the description of the aggressivity of a cancer disease, typically grading is used which is a system for classifying cancer cells in terms of how abnormal they appear when examined under a microscope. The objective of a grading system is to provide information about the probable growth rate of the tumor and its tendency to spread. The systems used to grade tumors vary with each type of cancer. Grading plays a role in treatment decisions.
Such grading systems are known to the ones skilled in the art. One of them is the Gleason score which is a system of grading prostate cancer tissue based on how it looks under a microscope. Gleason scores range from 2 to 10 and indicate how likely it is that a tumor will spread. A low Gleason score means the cancer tissue is similar to normal prostate tissue and the tumor is less likely to spread; a high Gleason score means the cancer tissue is very different from normal and the tumor is more likely to spread.
PKN3 which is also referred to as protein kinase N beta or PKN beta has been, among others, described by Oishi K, et al. (Oishi K. et al. Biochem. Biophys. Res. Commun. 261 (3): 808-14) or Shibata, H et al. (Shibata, H. et al.; J. Biochem. (Japan) 130 (1): 23-31). PKN3 has also been identified as a target molecule in tumors, in particular solid tumors, cancers, in particular metastatic cancers, and in pre-eclampsia. Also, as described in international patent application WO 2004/019973 protein kinase N beta is a downstream target of the PI-3 kinase/PTEN pathway which is linked to tumorigenesis and metastasis. Particularly the latter effect seems to be strongly related to the loss of suppressor function, more particularly PTEN tumour suppressor function.
The treatment of any disease is intended to provide relief or even cure to a patient while avoiding any undesired side effects or any adverse effects. In order to comply with this task there is a need for biomarkers which allow, in the broadest sense, to distinguish responders to a therapy from non-responders to such therapy. Furthermore, biomarkers are, for example, needed and useful as inclusion criterion for clinical trials, establishment or identification of optimum drug, dose and schedule of therapy and for identifying patients at high risk for adverse effects.
In the light of the above, there is a need for identifying biomarkers which can be used in the context of diseases and more specifically of diseases which can be treated by administering to a patient suffering from or being at risk of suffering from a disease which can be treated by a PKN3 inhibitor. Insofar, one problem underlying the present invention is the identification of such biomarkers.
A further problem underlying the present invention is the provision of a medicament for a particular group of patients suffering from or being at risk of suffering from a diseases which can be treated by administering to such patients a PKN3 inhibitor, whereby preferably such particular group of patients comprises a very high percentage of responders to such therapy comprising administering to the patients a PKN3 inhibitor.
These and further problems are solved by the subject matter of the attached independent claims. Particularly preferred embodiments may be taken from the attached dependent claims.
The problem underlying the present invention is also solved in a first aspect which is also the first embodiment of the first aspect by the use of VEGFR1 or of a nucleic acid coding for VEGFR1 as a biomarker in a method for the treatment of a subject, wherein the method for the treatment comprises administering to the subject a PKN3 inhibitor.
In a second embodiment of the first aspect which is also an embodiment of the first embodiment of the first aspect, the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1 is a or the biomarker.
The problem underlying the present invention is also solved in a second aspect which is also the first embodiment of the second aspect by the use of VEGFR1 or of a nucleic acid coding for VEGFR1 as a biomarker in designing a method for the treatment of a subject, wherein the method for the treatment comprises administering to the subject a PKN3 inhibitor.
In a second embodiment of the second aspect which is also an embodiment of the first embodiment of the second aspect, the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1 is a or the biomarker.
In a third embodiment of the first aspect which is also an embodiment of the first and the second embodiment of the first aspect, and in a third embodiment of the second aspect which is also an embodiment of the first and the second embodiment of the second aspect the VEGFR1 is selected from the group comprising VEGFR1 variant 2, VEGFR1 variant 1, VEGFR1 variant 3 and VEGFR1 variant 4.
In a fourth embodiment of the first aspect which is also an embodiment of the first, second and third embodiment of the first aspect, and in a fourth embodiment of the second aspect which is also an embodiment of the first, second and third embodiment of the second aspect the nucleic acid coding for VEGFR1 is selected from the group comprising VEGFR1 transcript variant 2, VEGFR1 transcript variant 1, VEGFR1 transcript variant 3 and VEGFR1 transcript variant 4.
In a fifth embodiment of the first aspect which is also an embodiment of the first, second, third and fourth embodiment of the first aspect, and in a fifth embodiment of the second aspect which is also an embodiment of the first, second, third and fourth embodiment of the second aspect the VEGFR1 is soluble VEGFR1 or VEGFR1 variant 2.
In a sixth embodiment of the first aspect which is also an embodiment of the fifth embodiment of the first aspect, and in a sixth embodiment of the second aspect which is also an embodiment of the fifth embodiment of the second aspect the soluble VEGFR1 or VEGFR1 variant 2 comprises an amino acid sequence according to SEQ ID NO:1 or is encoded by a nucleotide sequence according to SEQ ID NO: 2.
In a seventh embodiment of the first aspect which is also an embodiment of the first, second, third and fourth embodiment of the first aspect, and in a seventh embodiment of the second aspect which is also an embodiment of the first, second, third and fourth embodiment of the second aspect the nucleic acid coding for VEGFR1 is a nucleic acid coding for soluble VEGFR1 or VEGFR1 variant 2.
In an eighth embodiment of the first aspect which is also an embodiment of the seventh embodiment of the first aspect, and in an eighth embodiment of the second aspect which is also an embodiment of the seventh embodiment of the second aspect the nucleic acid coding for soluble VEGFR1 or VEGFR1 variant 2 comprises a nucleotide sequence according to SEQ ID NO:2 or a nucleotide sequence encoding an amino acid sequence according to SEQ ID NO: 1.
In a ninth embodiment of the first aspect which is also an embodiment of the first, second, third and fourth embodiment of the first aspect, and in a ninth embodiment of the second aspect which is also an embodiment of the first, second, third and fourth embodiment of the second aspect the VEGFR1 is VEGFR1 variant 1.
In a tenth embodiment of the first aspect which is also an embodiment of the ninth embodiment of the first aspect, and in a tenth embodiment of the second aspect which is also an embodiment of the ninth embodiment of the second aspect the VEGFR1 variant 1 comprises an amino acid sequence according to SEQ ID NO: 3 or is encoded by a nucleotide sequence according to SEQ ID NO: 4.
In an eleventh embodiment of the first aspect which is also an embodiment of the first, second, third and fourth embodiment of the first aspect, and in an eleventh embodiment of the second aspect which is also an embodiment of the first, second, third and fourth embodiment of the second aspect the nucleic acid coding for VEGFR1 is a nucleic acid coding for VEGFR1 variant 1.
In a twelfth embodiment of the first aspect which is also an embodiment of the eleventh embodiment of the first aspect, and in a twelfth embodiment of the second aspect which is also an embodiment of the eleventh embodiment of the second aspect the nucleic acid coding for VEGFR1 variant 1 comprises a nucleotide sequence according to SEQ ID NO: 4 or a nucleotide sequence encoding an amino acid sequence according to SEQ ID NO: 3.
In a 13th embodiment of the first aspect which is also an embodiment of the first, second, third and fourth embodiment of the first aspect, and in a 13th embodiment of the second aspect which is also an embodiment of the first, second, third and fourth embodiment of the second aspect the VEGFR1 is VEGFR1 variant 3.
In a 14th embodiment of the first aspect which is also an embodiment of the 13th embodiment of the first aspect, and in a 14th embodiment of the second aspect which is also an embodiment of the 13th embodiment of the second aspect the VEGFR1 variant 3 comprises an amino acid sequence according to SEQ ID NO: 5 or is encoded by a nucleotide sequence according to SEQ ID NO: 6.
In a 15th embodiment of the first aspect which is also an embodiment of the first, second, third and fourth embodiment of the first aspect, and in a 15th embodiment of the second aspect which is also an embodiment of the first, second, third and fourth embodiment of the second aspect the nucleic acid coding for VEGFR1 is a nucleic acid coding for VEGFR1 variant 3.
In a 16th embodiment of the first aspect which is also an embodiment of the 15th embodiment of the first aspect, and in a 16th embodiment of the second aspect which is also an embodiment of the 15th embodiment of the second aspect the nucleic acid coding for VEGFR1 variant 3 comprises a nucleotide sequence according to SEQ ID NO: 6 or a nucleotide sequence encoding an amino acid sequence according to SEQ ID NO: 5.
In a 17th embodiment of the first aspect which is also an embodiment of the first, second, third and fourth embodiment of the first aspect, and in a 17th embodiment of the second aspect which is also an embodiment of the first, second, third and fourth embodiment of the second aspect the VEGFR1 is VEGFR1 variant 4.
In an 18th embodiment of the first aspect which is also an embodiment of the 17th embodiment of the first aspect, and in an 18th embodiment of the second aspect which is also an embodiment of the 17th embodiment of the second aspect the VEGFR1 variant 4 comprises an amino acid sequence according to SEQ ID NO: 7 or is encoded by a nucleotide sequence according to SEQ ID NO: 8.
In a 19th embodiment of the first aspect which is also an embodiment of the first, second, third and fourth embodiment of the first aspect, and in a 19th embodiment of the second aspect which is also an embodiment of the first, second, third and fourth embodiment of the second aspect the nucleic acid coding for VEGFR1 is a nucleic acid coding for VEGFR1 variant 4.
In a 20th embodiment of the first aspect which is also an embodiment of the 19th embodiment of the first aspect, and in a 20th embodiment of the second aspect which is also an embodiment of the 19th embodiment of the second aspect the nucleic acid coding for VEGFR1 variant 4 comprises a nucleotide sequence according to SEQ ID NO: 8 or a nucleotide sequence encoding an amino acid sequence according to SEQ ID NO: 7.
In a 21st embodiment of the first aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th and 20th embodiment of the first aspect, and in a 21st embodiment of the second aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th and 20th embodiment of the second aspect the biomarker is a pharmacodynamic biomarker.
In a 22nd embodiment of the first aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th and 20th embodiment of the first aspect, and in a 22nd embodiment of the second aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th and 20th embodiment of the second aspect the biomarker is a predictive biomarker.
In a 23rd embodiment of the first aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th and 20th embodiment of the first aspect, and in a 23rd embodiment of the second aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th and 20th embodiment of the second aspect the biomarker is a prognostic biomarker.
In a 24th embodiment of the first aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th and 20th embodiment of the first aspect, and in a 24th embodiment of the second aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th and 20th embodiment of the second aspect the biomarker is a surrogate biomarker.
In a 25th embodiment of the first aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, 21st, 22nd, 23rd and 24th embodiment of the first aspect, and in a 25th embodiment of the second aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th and 20th, 21st, 22nd, 23rd and 24th embodiment of the second aspect the subject is suffering from or at risk of suffering from a disease, wherein the disease is a disease which can be treated, ameliorated and/or cured by a PKN3 inhibitor.
In a 26th embodiment of the first aspect which is also an embodiment of the 25th embodiment of the first aspect, and in a 26th embodiment of the second aspect which is also an embodiment of the 25th embodiment of the second aspect the disease is selected from the group comprising tumor diseases, cancer diseases and pre-eclampsia.
In a 27th embodiment of the first aspect which is also an embodiment of the 25th and 26th embodiment of the first aspect, and in a 27th embodiment of the second aspect which is also an embodiment of the 25th and 26th embodiment of the second aspect the disease is selected from the group comprising lung cancer, pancreas cancer, liver cancer, endometrial cancer, colorectal carcinomas, gliomas, adenocarcinomas, endometrial hyperplasias, hereditary non-polyposis colorectal carcinoma, breast-ovarian cancer, prostate cancer, gastrointestinal harmatomas, lipomas, thyroid adenomas, fibrocystic disease of the breast, cerebellar dysplastic gangliocytoma, breast and thyroid malignancies, large cell carcinoma, small cell carcinoma and squamous cell carcinoma.
In a 28th embodiment of the first aspect which is also an embodiment of the 25th and 26th embodiment of the first aspect, and in a 28th embodiment of the second aspect which is also an embodiment of the 25th and 26th embodiment of the second aspect the disease is a disease is selected from the group comprising cancers, metastatic cancers and any pathological conditions involving the PI 3-kinase pathway.
In a 29th embodiment of the first aspect which is also an embodiment of the 25th and 26th embodiment of the first aspect, and in a 29th embodiment of the second aspect which is also an embodiment of the 25th and 26th embodiment of the second aspect the disease is characterized in that the cells being involved in said disease lack PTEN activity, show an increased aggressive behavior, or are cells of a late stage tumor.
In a 30th embodiment of the first aspect which is also an embodiment of the 25th and 26th embodiment of the first aspect, and in a 30th embodiment of the second aspect which is also an embodiment of the 25th and 26th embodiment of the second aspect the disease is selected from the group comprising metastatic cancers and any pathological conditions involving the PI 3-kinase pathway, whereby such pathological condition consists of endometrial cancer, colorectal carcinomas, gliomas, adenocarcinomas, endometrial hyperplasias, Cowden's syndrome, hereditary non-polyposis colorectal carcinoma, Li-Fraumene's syndrome, breast-ovarian cancer, prostate cancer, Bannayan-Zonana syndrome, LDD (Lhermitte-Duklos' syndrome) hamartoma-macrocephaly diseases including Cow disease (CD) and Bannayan-Ruvalcaba-Rily syndrome (BRR), mucocutaneous lesions such as trichilemmonmas, macrocephaly, mental retardation, gastrointestinal harmatomas, lipomas, thyroid adenomas, fibrocystic disease of the breast, cerebellar dysplastic gangliocytoma, and breast and thyroid malignancies and large cell carcinoma, small cell carcinoma and squamous cell carcinoma.
In a 31st embodiment of the first aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, 21st, 22nd, 23rd, 24th, 25th, 26th, 27th, 28th, 29th and 30th embodiment of the first aspect, and in a 31st embodiment of the second aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, 21st, 22nd, 23rd, 24th, 25th, 26th, 27th, 28th, 29th and 30th embodiment of the second aspect the PKN3 inhibitor is selected from the group comprising an siRNA directed against an mRNA coding for PKN3, an antisense oligonucleotide directed against an mRNA coding for PKN3, a ribozyme directed against an mRNA coding for PKN3, an shRNA directed against an mRNA coding for PKN3, an miRNA or antagomir directed against an mRNA coding for PKN3, an aptamer directed against PKN3, a spiegelmer directed against PKN3, an antibody directed against PKN3, an anticalin directed against PKN3, and a small molecule.
In a 32nd embodiment of the first aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, 21st, 22nd, 23rd, 24th, 25th, 26th, 27th, 28th, 29th, 30th and 31st embodiment of the first aspect, and in a 32nd embodiment of the second aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, 21st, 22nd, 23rd, 24th, 25th, 26th, 27th, 28th, 29th, 30th and 31st embodiment of the second aspect the PKN3 inhibitor is an siRNA wherein the siRNA is as follows:









(SEQ ID NO: 11)



5′ 5u8u7c6g8a6g5c7u7a6g5c5 3′



 



(SEQ ID NO: 12)



3′ a6c6g8u7c5u7a8g6g5u7a8a 5′






with unmodified ribonucleotides being as indicated and modified ribonucleotides being represented as follows:

5: 2′-O-Methyl-u,
6: 2′-O-Methyl-a,
7: 2′-O-Methyl-c,
8: 2′-O-Methyl-g.
In a 33rd embodiment of the first aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, 21st, 22nd, 23rd, 24th, 25th, 26th, 27th, 28th, 29th and 30th, 31st and 32nd embodiment of the first aspect, and in a 33rd embodiment of the second aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, 21st, 22nd, 23rd, 24th, 25th, 26th, 27th, 28th, 29th and 30th, 31st and 32nd embodiment of the second aspect PKN3 comprises an amino acid sequence according to SEQ ID NO: 9.
In a 34th embodiment of the first aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, 21st, 22nd, 23rd, 24th, 25th, 26th, 27th, 28th, 29th and 30th, 31st and 32nd embodiment of the first aspect, and in a 34th embodiment of the second aspect which is also an embodiment of the first, second, third, fourth, fifth, sixth, seventh, eighth, ninth tenth, eleventh, twelfth, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, 21st, 22nd, 23rd, 24th, 25th, 26th, 27th, 28th, 29th and 30th, 31st and 32nd embodiment of the second aspect PKN3 is encoded by a nucleotide sequence according to SEQ ID NO: 10 or a nucleotide sequence coding for an amino acid sequence according to SEQ ID NO: 9.
Additional non-limiting embodiments provide:
1. Use of VEGFR1 or of a nucleic acid coding for VEGFR1 as a biomarker in a method for the treatment of a subject, wherein the method for the treatment comprises administering to the subject a PKN3 inhibitor.
2. Use according to embodiment 1, wherein the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1 is a or the biomarker.
3. Use of VEGFR1 or of a nucleic acid coding for VEGFR1 as a biomarker in designing a method for the treatment of a subject, wherein the method for the treatment comprises administering to the subject a PKN3 inhibitor.
4. Use according to embodiment 3, wherein the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1 is a or the biomarker.
5. Use according to any one of embodiments 1 to 4, wherein the VEGFR1 is selected from the group comprising VEGFR1 variant 2, VEGFR1 variant 1, VEGFR1 variant 3 and VEGFR1 variant 4.
6. Use according to any one of embodiments 1 to 4, wherein the nucleic acid coding for VEGFR1 is selected from the group comprising VEGFR1 transcript variant 2, VEGFR1 transcript variant 1, VEGFR1 transcript variant 3 and VEGFR1 transcript variant 4.
7. Use according to any one of embodiments 1 to 6, wherein the VEGFR1 is soluble VEGFR1 or VEGFR1 variant 2.
8. Use according to embodiment 7, wherein the soluble VEGFR1 or VEGFR1 variant 2 comprises an amino acid sequence according to SEQ ID NO:1 or is encoded by a nucleotide sequence according to SEQ ID NO: 2.
9. Use according to any one of embodiments 1 to 6, wherein the nucleic acid coding for VEGFR1 is a nucleic acid coding for soluble VEGFR1 or VEGFR1 variant 2.
10. Use according to embodiment 9, wherein the nucleic acid coding for soluble VEGFR1 or VEGFR1 variant 2 comprises a nucleotide sequence according to SEQ ID NO:2 or a nucleotide sequence encoding an amino acid sequence according to SEQ ID NO: 1.
11. Use according to any one of embodiments 1 to 6, wherein the VEGFR1 is VEGFR1 variant 1.
12. Use according to embodiment 11, wherein the VEGFR1 variant 1 comprises an amino acid sequence according to SEQ ID NO: 3 or is encoded by a nucleotide sequence according to SEQ ID NO: 4.
13. Use according to any one of embodiments 1 to 6, wherein the nucleic acid coding for VEGFR1 is a nucleic acid coding for VEGFR1 variant 1.
14. Use according to embodiment 13, wherein the nucleic acid coding for VEGFR1 variant 1 comprises a nucleotide sequence according to SEQ ID NO: 4 or a nucleotide sequence encoding an amino acid sequence according to SEQ ID NO: 3.
15. Use according to any one of embodiments 1 to 6, wherein the VEGFR1 is VEGFR1 variant 3.
16. Use according to embodiment 15, wherein the VEGFR1 variant 3 comprises an amino acid sequence according to SEQ ID NO: 5 or is encoded by a nucleotide sequence according to SEQ ID NO: 6.
17. Use according to any one of embodiments 1 to 6, wherein the nucleic acid coding for VEGFR1 is a nucleic acid coding for VEGFR1 variant 3.
18. Use according to embodiment 17, wherein the nucleic acid coding for VEGFR1 variant 3 comprises a nucleotide sequence according to SEQ ID NO: 6 or a nucleotide sequence encoding an amino acid sequence according to SEQ ID NO: 5.
19. Use according to any one of embodiments 1 to 6, wherein the VEGFR1 is VEGFR1 variant 4.
20. Use according to embodiment 19, wherein the VEGFR1 variant 4 comprises an amino acid sequence according to SEQ ID NO: 7 or is encoded by a nucleotide sequence according to SEQ ID NO: 8.
21. Use according to any one of embodiments 1 to 6, wherein the nucleic acid coding for VEGFR1 is a nucleic acid coding for VEGFR1 variant 4.
22. Use according to embodiment 21, wherein the nucleic acid coding for VEGFR1 variant 4 comprises a nucleotide sequence according to SEQ ID NO: 8 or a nucleotide sequence encoding an amino acid sequence according to SEQ ID NO: 7.
23. Use according to any one of embodiments 1 to 22, wherein the biomarker is a pharmacodynamic biomarker.
24. Use according to any one of embodiments 1 to 22, wherein the biomarker is a predictive biomarker.
25. Use according to any one of embodiments 1 to 22, wherein the biomarker is a prognostic biomarker.
26. Use according to any one of embodiments 1 to 22, wherein the biomarker is a surrogate biomarker.
27. Use according to any one of embodiments 1 to 26, wherein the subject is suffering from or at risk of suffering from a disease, wherein the disease is a disease which can be treated, ameliorated and/or cured by a PKN3 inhibitor.
28. Use according to embodiment 27, wherein the disease is selected from the group comprising tumor diseases, cancer diseases and pre-eclampsia.
29. Use according to any one of embodiments 27 to 28, wherein the disease is selected from the group comprising lung cancer, pancreas cancer, liver cancer, endometrial cancer, colorectal carcinomas, gliomas, adenocarcinomas, endometrial hyperplasias, hereditary non-polyposis colorectal carcinoma, breast-ovarian cancer, prostate cancer, gastrointestinal harmatomas, lipomas, thyroid adenomas, fibrocystic disease of the breast, cerebellar dysplastic gangliocytoma, breast and thyroid malignancies, large cell carcinoma, small cell carcinoma and squamous cell carcinoma.
30. Use according to any one of embodiments 27 to 28, wherein the disease is a disease is selected from the group comprising cancers, metastatic cancers and any pathological conditions involving the PI 3-kinase pathway.
31. Use according to any one of embodiments 27 to 28, wherein the disease is characterized in that the cells being involved in said disease lack PTEN activity, show an increased aggressive behavior, or are cells of a late stage tumor.
32. Use according to any one of embodiments 27 to 28, wherein the disease is selected from the group comprising metastatic cancers and any pathological conditions involving the PI 3-kinase pathway, whereby such pathological condition consists of endometrial cancer, colorectal carcinomas, gliomas, adenocarcinomas, endometrial hyperplasias, Cowden's syndrome, hereditary non-polyposis colorectal carcinoma, Li-Fraumene's syndrome, breast-ovarian cancer, prostate cancer, Bannayan-Zonana syndrome, LDD (Lhermitte-Duklos' syndrome) hamartoma-macrocephaly diseases including Cow disease (CD) and Bannayan-Ruvalcaba-Rily syndrome (BRR), mucocutaneous lesions such as trichilemmonmas, macrocephaly, mental retardation, gastrointestinal harmatomas, lipomas, thyroid adenomas, fibrocystic disease of the breast, cerebellar dysplastic gangliocytoma, and breast and thyroid malignancies and large cell carcinoma, small cell carcinoma and squamous cell carcinoma.
33. Use according to any one of embodiments 1 to 32, wherein the PKN3 inhibitor selected from the group comprising an siRNA directed against an mRNA coding for PKN3, an antisense oligonucleotide directed against an mRNA coding for PKN3, a ribozyme directed against an mRNA coding for PKN3, an shRNA directed against an mRNA coding for PKN3, an miRNA or antagomir directed against an mRNA coding for PKN3, an aptamer directed against PKN3, a spiegelmer directed against PKN3, an antibody directed against PKN3, an anticalin directed against PKN3, and a small molecule.
34. Use according to any one of embodiments 1 to 33, wherein the PKN3 inhibitor is an siRNA wherein the siRNA is as follows:









(SEQ ID NO: 11)



5′ 5u8u7c6g8a6g5c7u7a6g5c5 3′



 



(SEQ ID NO: 12)



3′ a6c6g8u7c5u7a8g6g5u7a8a 5′






with unmodified ribonucleotides being as indicated and modified ribonucleotides being represented as follows:

5: 2′-O-Methyl-u,
6: 2′-O-Methyl-a,
7: 2′-O-Methyl-c,
8: 2′-O-Methyl-g.
35. Use according to any one of embodiments 1 to 34, wherein PKN3 comprises an amino acid sequence according to SEQ ID NO: 9.
36. Use according to any one of embodiments 1 to 34, wherein PKN3 is encoded by a nucleotide sequence according to SEQ ID NO: 10 or a nucleotide sequence coding for an amino acid sequence according to SEQ ID NO: 9.
37. A method for deciding whether a subject is a responder to a method of treatment, wherein the method of treatment comprises administering to the subject a PKN3 inhibitor, comprising:

    
    
        determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject prior to the subject being subjected to the method of treatment,
        determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject after the subject having been subjected to the method of treatment; wherein if the level of VEGFR1 or a nucleic acid coding for VEGFR1 in a sample from the subject after the subject having been subjected to the method of treatment is decreased compared to the level of VEGFR1 or a nucleic acid coding for VEGFR1 in a sample from the subject prior to the subject having being subjected to the method of treatment, the subject is a responder to the method of treatment.
    
    


38. The method according to embodiment 37, wherein the decrease is a decrease of 10% or more, of 20% or more, 40% or more, 60% or more or 80% or more.
39. The method according to any one of embodiments 37 to 38, wherein the subject is suffering from a disease or is at risk of suffering from a disease and wherein the method of treatment is a method of treatment for the disease.
40. A method for deciding whether a subject having undergone a first method of treatment, wherein the first method of treatment comprises administering to the subject a PKN3 inhibitor, shall be subject to a second method of treatment, wherein the second method of treatment comprises administering to the subject a PKN3 inhibitor, comprising:

    
    
        determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject prior to a first method of treatment,
        determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject after a first period of time after the first method of treatment, and
        optionally determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject after a second period of time after the first method of treatment,

wherein if the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject after the first or second period of time after the first method of treatment is increased compared to the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject prior to a first method of treatment, the subject is to be subjected to the second method of treatment.

    
    


41. The method according to embodiment 40, wherein the increase is 100% or more, 80% or more, 60% or more or 40% or more.
42. The method according to any one of embodiments 40 to 41, wherein the subject is suffering from a disease or is at risk of suffering from a disease and wherein the method of treatment is a method of treatment for the disease.
43. The method according to any one of embodiments 40 to 41, wherein first period of time after the first method of treatment is about 24 hours or 48 hours after the last administration of the PKN3 inhibitor being part of the first method of treatment.
44. The method according to any of embodiments 40 to 41, wherein the second period of time after the first method of treatment starts about 1 or two months after the first period of time after the first method of treatment.
45. The method according to any one of embodiments 40 to 44, wherein the first method of treatment is the same as the second method of treatment, or wherein the first method of treatment is different from the second method of treatment.
46. A method for deciding whether a subject shall undergo a method of treatment, whereby the method of treatment comprises the administration of a PKN3 inhibitor, comprising determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1, or determining the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, wherein if the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, expressed as titre of VEGF1 in blood or plasma of the subject, is equal to or greater than 200 pg/ml, the patient is amenable to the method of treatment comprising administration of a PKN3 inhibitor.
47. The method according to embodiment 46, wherein if the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, expressed as titre of VEGF1 in blood or plasma of the subject, is equal to or greater than 400 pg/ml, preferably equal to or greater than 600 pg/ml, more preferably equal to or greater than 800 pg/ml, the patient is amenable to the method of treatment comprising administration of a PKN3 inhibitor.
48. The method according to any one of embodiments 37 to 47, wherein the disease is any disease as defined in any of the preceding embodiments.
49. The method according to any one of embodiments 37 to 48, wherein the PKN3 inhibitor is any PKN3 inhibitor as defined in any of the preceding embodiments.
50. The method according to any one of embodiments 37 to 49, wherein the VEGFR1 or a nucleic acid coding thereof is any VEGFR1 or a nucleic acid coding for the VEGFR1 as defined in any of the preceding embodiments.
51. A PKN3 inhibitor for use in a method for the treatment of a subject suffering from or being at risk of suffering from a disease, wherein the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, expressed as titre of VEGF1 in blood or plasma of the subject, is equal to or greater than 200 pg/ml.
52. The PKN3 inhibitor according to embodiment 51, wherein the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, expressed as titre of VEGF1 in blood or plasma of the subject, is equal to or greater than 400 pg/ml, preferably equal to or greater than 600 pg/ml and more preferably equal to or greater than 800 pg/ml.
The problem underlying the present invention is also solved in a third aspect which is also the first embodiment of the third aspect by a method for deciding whether a subject is a responder to a method of treatment, wherein the method of treatment comprises administering to the subject a PKN3 inhibitor, comprising:
determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject prior to the subject being subjected to the method of treatment,
determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject after the subject having been subjected to the method of treatment;
wherein if the level of VEGFR1 or a nucleic acid coding for VEGFR1 in a sample from the subject after the subject having been subjected to the method of treatment is decreased compared to the level of VEGFR1 or a nucleic acid coding for VEGFR1 in a sample from the subject prior to the subject having being subjected to the method of treatment, the subject is a responder to the method of treatment.
In a second embodiment of the third aspect which is also an embodiment of the first embodiment of the third aspect, the decrease is a decrease of 10% or more, of 20% or more, 40% or more, 60% or more or 80% or more.
In a third embodiment of the third aspect which is also an embodiment of the first and the second embodiment of the third aspect, the subject is suffering from a disease or is at risk of suffering from a disease and wherein the method of treatment is a method of treatment for the disease.
The problem underlying the present invention is also solved in a fourth aspect which is also the first embodiment of the fourth aspect by a method for deciding whether a subject having undergone a first method of treatment, wherein the first method of treatment comprises administering to the subject a PKN3 inhibitor, shall be subject to a second method of treatment, wherein the second method of treatment comprises administering to the subject a PKN3 inhibitor, comprising:
determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject prior to a first method of treatment,
determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject after a first period of time after the first method of treatment, and
optionally determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject after a second period of time after the first method of treatment,
wherein if the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject after the first or second period of time after the first method of treatment is increased compared to the level of VEGFR1 or of a nucleic acid coding for VEGFR1 in a sample from the subject prior to a first method of treatment, the subject is to be subjected to the second method of treatment.
In a second embodiment of the fourth aspect which is also an embodiment of the first embodiment of the fourth aspect, the increase is 100% or more, 80% or more, 60% or more or 40% or more.
In a third embodiment of the fourth aspect which is also an embodiment of the first and the second embodiment of the fourth aspect, the subject is suffering from a disease or is at risk of suffering from a disease and wherein the method of treatment is a method of treatment for the disease.
In a fourth embodiment of the fourth aspect which is also an embodiment of the first, second and third embodiment of the fourth aspect, the first period of time after the first method of treatment is about 24 hours or 48 hours after the last administration of the PKN3 inhibitor being part of the first method of treatment.
In a fifth embodiment of the fourth aspect which is also an embodiment of the first, second and third embodiment of the fourth aspect, the second period of time after the first method of treatment starts about 1 or two months after the first period of time after the first method of treatment.
In a sixth embodiment of the fourth aspect which is also an embodiment of the first, second, third, fourth and fifth embodiment of the fourth aspect, the first method of treatment is the same as the second method of treatment, or wherein the first method of treatment is different from the second method of treatment.
The problem underlying the present invention is also solved in a fifth aspect which is also the first embodiment of the fifth aspect by a method for deciding whether a subject shall undergo a method of treatment, whereby the method of treatment comprises the administration of a PKN3 inhibitor, comprising determining the level of VEGFR1 or of a nucleic acid coding for VEGFR1, or determining the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, wherein if the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, expressed as titre of VEGF1 in blood or plasma of the subject, is equal to or greater than 200 pg/ml, the patient is amenable to the method of treatment comprising administration of a PKN3 inhibitor.
In a second embodiment of the fifth aspect which is also an embodiment of the first embodiment of the fifth aspect, if the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, expressed as titre of VEGF1 in blood or plasma of the subject, is equal to or greater than 400 pg/ml, preferably equal to or greater than 600 pg/ml, more preferably equal to or greater than 800 pg/ml, the patient is amenable to the method of treatment comprising administration of a PKN3 inhibitor.
In an embodiment of any embodiment of the third, fourth and fifth aspect the disease is any disease as defined in any of the embodiments of any aspect of the present invention.
In an embodiment of any embodiment of the third, fourth and fifth aspect the PKN3 inhibitor is any PKN3 inhibitor as defined in any of the embodiments of any aspect of the present invention.
In an embodiment of any embodiment of the third, fourth and fifth aspect the VEGFR1 or a nucleic acid coding thereof is any VEGFR1 or a nucleic acid coding for the VEGFR1 as defined in any of the embodiments of any aspect of the present invention.
The problem underlying the present invention is also solved in a sixth aspect which is also the first embodiment of the sixth aspect by a PKN3 inhibitor for use in a method for the treatment of a subject suffering from or being at risk of suffering from a disease, wherein the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, expressed as titre of VEGF1 in blood or plasma of the subject, is equal to or greater than 200 pg/ml.
In a second embodiment of the sixth aspect which is also an embodiment of the sixth embodiment of the second aspect, the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1, expressed as titre of VEGF1 in blood or plasma of the subject, is equal to or greater than 400 pg/ml, preferably equal to or greater than 600 pg/ml and more preferably equal to or greater than 800 pg/ml.
The present invention, in its various aspects, is based on the surprising finding that VEGFR1 or a nucleic acid coding for VEGFR1, i.e. VEGF receptor 1 which is also referred to as Flt-1, is a biomarker for therapies which are different from antiangiogenic therapy. More specifically, the present invention is based on the surprising finding that VEGFR1 is a biomarker in connection with methods for the treatment of a subject, wherein the method for the treatment comprises administering to the subject a PKN3 inhibitor. Based on this finding it is also within the present invention that VEGFR1 or a nucleic acid coding therefor are used as a biomarker in a method for the treatment of a subject or in connection with designing a method for the treatment of a subject, wherein the method for the treatment comprises administering to the subject a PKN3 inhibitor. Such designing may comprise, among other, at least one of the following: Identifying responders from non-responders to the method for the treatment comprising administering a PKN3 inhibitor, defining the establishment or identification of optimum drug, dose and schedule of such method for the treatment and for identifying patients at high risk for adverse effects in connection with such method for the treatment.
As preferably used herein, a method for the treatment means a therapy and a method for the treatment comprising administration to a subject a PKN3 inhibitor means an anti-PKN3 therapy.
As preferably used herein, a PKN3 inhibitor is a compound which addresses or targets PKN3 or a fragment thereof, whereby the targeting of PKN3 or a fragment thereof results in a therapeutic effect in a subject to which the PKN3 inhibitor is administered.
A subject as preferably used is a vertebrate, more preferably a mammal. A particular preferred subject is man.
It will be understood by a person skilled in the art that the use of VEGFR1 or of a nucleic acid coding for VEGFR1 as a biomarker can be realized or put into practice by using or referring to the expression level of VEGFR1 or the expression level of a nucleic acid coding for VEGFR1. Insofar, the present invention in its various aspects also relates to the use of the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1 as a biomarker in a method for the treatment of a subject, wherein the method for the treatment comprises administering to the subject a PKN3 inhibitor, and to the use of the expression level of VEGFR1 or of a nucleic acid coding for VEGFR1 as a biomarker in a method for designing or in designing a method for the treatment of a subject, wherein the method for the treatment comprises administering to the subject a PKN3 inhibitor.
In accordance with the present invention, in its various aspects, either VEGFR1, i.e. the protein, or a nucleic acid which codes for VEGFR1 is used as a biomarker or is used in the methods and products of the present invention. It will be acknowledged by a person skilled in the art that, at the level of the nucleic acid, there are a total of four different transcript variants for VEGFR1, namely VEGFR1 transcript variant 2, VEGFR1 transcript variant 1, VEGFR1 transcript variant 3 and VEGFR1 transcript variant 4. It is understood that VEGFR1 transcript 2 codes for soluble VEGFR1 and VEGFR1 transcript 1 codes for the membrane-bound VEGFR1. VEGFR1 transcripts 3 and 4 code for fragments of VEGFR1. It is within the present invention that any of the VEGFR1 transcript variants 1 to 4 is, in principle, suitable for use in connection with the present invention. It is also within the present invention that any of the VEGFR1 variants 1 to 4 is, in principle suitable for use in connection with the various aspects of the present invention. As preferably used herein, a VEGFR1 variant 1 is a protein encoded by VEGFR1 splice variant 1, a VEGFR1 variant 2 is a protein encoded by VEGFR1 splice variant 2, a VEGFR1 variant 3 is a protein encoded by VEGFR1 splice variant 3, and a VEGFR1 variant 4 is a protein encoded by VEGFR1 splice variant 4.
As preferably used herein in connection with any aspect of the present invention a pharmacodynamics biomarker is a biomarker whose changes after treatment are associated with target modulation by a specific agent.
As preferably used herein in connection with any aspect of the present invention a predictive biomarker is a biomarker which can be used in advance of therapy to estimate response or survival of a specific patient on a specific treatment compared with another treatment.
As preferably used herein in connection with any aspect of the present invention a prognostic biomarker is a biomarker which provides information about the patient's overall disease outcome, regardless of therapy.
As preferably used herein in connection with any aspect of the present invention a surrogate biomarker is a biomarker intended to substitute for a clinical end point.
Whether a disease is a disease which can be treated, ameliorated and/or cured by a PKN3 inhibitor, can be determined by a person skilled in the art using routine methods and routine tests. For example, a person skilled in the art will use appropriate animal models, or any surrogate test system, and apply to such animal model or surrogate test system a PKN3 inhibitor and check whether the required read-out can be observed which goes along with the effect(s) of a PKN3 inhibitor. For example, such test may be the matrigel test described in international patent application WO 2008/009477, or any other tumor or cancer growth system involving PKN3 as a target molecule.
Preferably, a disease as used in the various aspects of the present invention is one which is selected from the group comprising:
A
Acute Lymphoblastic Leukemia (ALL)
Acute Myeloid Leukemia (AML)
Adolescents, Cancer in
Adrenocortical Carcinoma
Childhood
AIDS-Related Cancers
Kaposi Sarcoma
Lymphoma
Anal Cancer
Appendix Cancer
Astrocytomas, Childhood
Atypical Teratoid/Rhabdoid Tumor, Childhood, Central Nervous System
B
Basal Cell Carcinoma—see Skin Cancer (Nonmelanoma)
Bile Duct Cancer, Extrahepatic
Bladder Cancer
Childhood
Bone Cancer, Osteosarcoma and Malignant Fibrous Histiocytoma
Brain Stem Glioma, Childhood
Brain Tumor
Astrocytomas, Childhood
Brain and Spinal Cord Tumors, Childhood
Brain Stem Glioma, Childhood
Central Nervous System Atypical Teratoid/Rhabdoid Tumor, Childhood
Central Nervous System Embryonal Tumors, Childhood
Central Nervous System Germ Cell Tumors, Childhood
Craniopharyngioma, Childhood
Ependymoblastoma, Childhood
Ependymoma, Childhood
Medulloblastoma, Childhood
Medulloepithelioma, Childhood
Pineal Parenchymal Tumors of Intermediate Differentiation, Childhood
Supratentorial Primitive Neuroectodermal Tumors and Pineoblastoma, Childhood
Breast Cancer
Childhood
Male
Pregnancy, Breast Cancer and
Bronchial Tumors, Childhood
Burkitt Lymphoma—see Non-Hodgkin Lymphoma
C
Carcinoid Tumor
Childhood
Gastrointestinal
Carcinoma of Unknown Primary
Childhood
Central Nervous System
Atypical Teratoid/Rhabdoid Tumor, Childhood
Embryonal Tumors, Childhood
Germ Cell Tumor, Childhood
Lymphoma, Primary
Cervical Cancer
Childhood
Childhood Cancers
Chordoma, Childhood
Chronic Lymphocytic Leukemia (CLL)
Chronic Myelogenous Leukemia (CML)
Chronic Myeloproliferative Disorders
Colon Cancer
Colorectal Cancer
Childhood
Craniopharyngioma, Childhood
Cutaneous T-Cell Lymphoma—see Mycosis Fungoides and Sézary Syndrome
D
Duct, Bile, Extrahepatic
Ductal Carcinoma In Situ (DCIS)
E
Embryonal Tumors, Central Nervous System, Childhood
Endometrial Cancer
Ependymoblastoma, Childhood
Ependymoma, Childhood
Esophageal Cancer
Childhood
Esthesioneuroblastoma, Childhood
Ewing Sarcoma Family of Tumors
Extracranial Germ Cell Tumor, Childhood
Extragonadal Germ Cell Tumor
Extrahepatic Bile Duct Cancer
Eye Cancer
Intraocular Melanoma
Retinoblastoma
F
Fibrous Histiocytoma of Bone, Malignant, and Osteosarcoma
G
Gallbladder Cancer
Gastric (Stomach) Cancer
Childhood
Gastrointestinal Carcinoid Tumor
Gastrointestinal Stromal Tumors (GIST)—see Soft Tissue Sarcoma
Germ Cell Tumor
Central Nervous System, Childhood
Extracranial, Childhood
Extragonadal
Ovarian
Gestational Trophoblastic Tumor
Glioma—see Brain Tumor
Childhood Brain Stem
H
Hairy Cell Leukemia
Head and Neck Cancer
Childhood
Heart Cancer, Childhood
Hepatocellular (Liver) Cancer
Histiocytosis, Langerhans Cell
Hodgkin Lymphoma
Hypopharyngeal Cancer
I
Intraocular Melanoma
Islet Cell Tumors, Pancreatic Neuroendocrine Tumors
K
Kaposi Sarcoma
Kidney
Renal Cell
L
Langerhans Cell Histiocytosis
Laryngeal Cancer
Childhood
Leukemia
Acute Lymphoblastic (ALL)
Acute Myeloid (AML)
Chronic Lymphocytic (CLL)
Chronic Myelogenous (CML)
Hairy Cell
Lip and Oral Cavity Cancer
Liver Cancer (Primary)
Lobular Carcinoma In Situ (LCIS)
Lung Cancer
Non-Small Cell
Small Cell
Lymphoma
AIDS-Related
Burkitt—see Non-Hodgkin Lymphoma
Cutaneous T-Cell—see Mycosis Fungoides and Sézary Syndrome
Hodgkin
Non-Hodgkin
Primary Central Nervous System (CNS)
M
Macroglobulinemia, Waldenström
Male Breast Cancer
Malignant Fibrous Histiocytoma of Bone and Osteosarcoma
Medulloblastoma, Childhood
Medulloepithelioma, Childhood
Melanoma
Childhood
Intraocular (Eye)
Merkel Cell Carcinoma
Mesothelioma, Malignant
Childhood
Metastatic Squamous Neck Cancer with Occult Primary
Midline Tract Carcinoma Involving NUT Gene
Mouth Cancer
Multiple Endocrine Neoplasia Syndromes, Childhood
Multiple Myeloma/Plasma Cell Neoplasm
Mycosis Fungoides
Myelodysplastic Syndromes
Myelodysplastic/Myeloproliferative Neoplasms
Myelogenous Leukemia, Chronic (CML)
Myeloid Leukemia, Acute (AML)
Myeloma, Multiple
Myeloproliferative Disorders, Chronic
N
Nasal Cavity and Paranasal Sinus Cancer
Nasopharyngeal Cancer
Childhood
Neuroblastoma
Non-Hodgkin Lymphoma
Non-Small Cell Lung Cancer
O
Oral Cancer
Childhood
Oral Cavity Cancer, Lip and
Oropharyngeal Cancer
Osteosarcoma and Malignant Fibrous Histiocytoma of Bone
Ovarian Cancer
Childhood
Epithelial
Germ Cell Tumor
Low Malignant Potential Tumor
P
Pancreatic Cancer
Childhood
Pancreatic Neuroendocrine Tumors (Islet Cell Tumors)
Papillomatosis, Childhood
Paraganglioma
Paranasal Sinus and Nasal Cavity Cancer
Parathyroid Cancer
Penile Cancer
Pharyngeal Cancer
Pheochromocytoma
Pineal Parenchymal Tumors of Intermediate Differentiation, Childhood
Pineoblastoma and Supratentorial Primitive Neuroectodermal Tumors, Childhood
Pituitary Tumor
Plasma Cell Neoplasm/Multiple Myeloma
Pleuropulmonary Blastoma, Childhood
Pregnancy and Breast Cancer
Primary Central Nervous System (CNS) Lymphoma
Prostate Cancer
R
Rectal Cancer
Renal Cell (Kidney) Cancer
Renal Pelvis and Ureter, Transitional Cell Cancer
Retinoblastoma
Rhabdomyosarcoma, Childhood
S
Salivary Gland Cancer
Childhood
Sarcoma
Ewing Sarcoma Family of Tumors
Kaposi
Soft Tissue
Uterine
Sézary Syndrome
Skin Cancer
Childhood
Melanoma
Merkel Cell Carcinoma
Nonmelanoma
Small Cell Lung Cancer
Small Intestine Cancer
Soft Tissue Sarcoma
Squamous Cell Carcinoma—see Skin Cancer (Nonmelanoma)
Squamous Neck Cancer with Occult Primary, Metastatic
Stomach (Gastric) Cancer
Childhood
Supratentorial Primitive Neuroectodermal Tumors, Childhood
T
T-Cell Lymphoma, Cutaneous—see Mycosis Fungoides and Sézary Syndrome
Testicular Cancer
Childhood
Throat Cancer
Thymoma and Thymic Carcinoma
Childhood
Thyroid Cancer
Childhood
Transitional Cell Cancer of the Renal Pelvis and Ureter
Trophoblastic Tumor, Gestational
U
Unknown Primary, Carcinoma of
Childhood
Unusual Cancers of Childhood
Ureter and Renal Pelvis, Transitional Cell Cancer
Urethral Cancer
Uterine Cancer, Endometrial
Uterine Sarcoma
V
Vaginal Cancer
Childhood
Vulvar Cancer
W
Waldenström Macroglobulinemia
Wilms Tumor
Women's Cancers
Y
Young Adults, Cancer in
as may be taken from the list of cancers provided by the National Cancer Institute at the National Institutes of Health.
In each and any aspect of the present invention the PKN3 inhibitor may be a compound which is selected from the group comprising an siRNA directed against an mRNA coding for PKN3, an antisense oligonucleotide directed against an mRNA coding for PKN3, a ribozyme directed against an mRNA coding for PKN3, an shRNA directed against an mRNA coding for PKN3, an miRNA or antagomir directed against an mRNA coding for PKN3, an aptamer directed against PKN3, a spiegelmer directed against PKN3, an antibody directed against PKN3, an anticalin directed against PKN3, a small molecule. Each and any of the above classes of compounds are known to a person skilled in the art and a PKN3 inhibitor of each any of said classes can be generated by a person skilled in the art by applying standard technology.
The manufacture of an antibody specific for VEGFR1 in its diverse forms is known to the one skilled in the art and, for example, described in Harlow, E., and Lane, D., “Antibodies: A Laboratory Manual,” Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1988). Preferably, monoclonal antibodies may be used in connection with the present invention which may be manufactured according to the protocol of Cesar and Milstein and further developments based thereon. Antibodies as used herein, include, but are not limited to, complete antibodies, antibody fragments or derivatives such as Fab fragments, Fc fragments and single-stranded antibodies, as long as they are suitable and capable of binding to VEGFR1 as disclosed herein. Apart from monoclonal antibodies also polyclonal antibodies may be used and/or generated. The generation of polyclonal antibodies is also known to the one skilled in the art and, for example, described in Harlow, E., and Lane, D., “Antibodies: A Laboratory Manual,” Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1988). Preferably, the antibodies used for therapeutical purposes are humanized or human antibodies as defined above.
The antibodies which may be used according to the present invention may have one or several markers or labels. Such markers or labels may be useful to detect the antibody either in its diagnostic application or its therapeutic application. Preferably the markers and labels are selected from the group comprising avidine, streptavidine, biotin, gold and fluorescein and used, e.g., in ELISA methods. These and further markers as well as methods are, e.g. described in Harlow, E., and Lane, D., “Antibodies: A Laboratory Manual,” Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1988).
“Anticalins” are, among others, described in German patent application DE 197 42 706.
Aptamers are D-nucleic acids which are either single stranded or double stranded and which specifically interact with a target molecule. The manufacture or selection of aptamers is, e.g., described in European patent EP 0 533 838. Basically the following steps are realized. First, a mixture of nucleic acids, i.e. potential aptamers, is provided whereby each nucleic acid typically comprises a segment of several, preferably at least eight subsequent randomised nucleotides. This mixture is subsequently contacted with the target molecule whereby the nucleic acid(s) bind to the target molecule, such as based on an increased affinity towards the target or with a bigger force thereto, compared to the candidate mixture. The binding nucleic acid(s) are/is subsequently separated from the remainder of the mixture. Optionally, the thus obtained nucleic acid(s) is amplified using, e.g. polymerase chain reaction. These steps may be repeated several times giving at the end a mixture having an increased ratio of nucleic acids specifically binding to the target from which the final binding nucleic acid is then optionally selected. These specifically binding nucleic acid(s) are referred to aptamers. It is obvious that at any stage of the method for the generation or identification of the aptamers samples of the mixture of individual nucleic acids may be taken to determine the sequence thereof using standard techniques. It is within the present invention that the aptamers may be stabilized such as, e.g., by introducing defined chemical groups which are known to the one skilled in the art of generating aptamers. Such modification may for example reside in the introduction of an amino group at the 2′-position of the sugar moiety of the nucleotides. Aptamers are currently used as therapeutical agents. However, it is also within the present invention that the thus selected or generated aptamers may be used for target validation and/or as lead substance for the development of medicaments, preferably of medicaments based on small molecules. This is actually done by a competition assay whereby the specific interaction between the target molecule and the aptamer is inhibited by a candidate drug whereby upon replacement of the aptamer from the complex of target and aptamer it may be assumed that the respective drug candidate allows a specific inhibition of the interaction between target and aptamer, and if the interaction is specific, said candidate drug will, at least in principle, be suitable to block the target and thus decrease its biological availability or activity in a respective system comprising such target. The thus obtained small molecule may then be subject to further derivatisation and modification to optimise its physical, chemical, biological and/or medical characteristics such as toxicity, specificity, biodegradability and bioavailability.
The generation or manufacture of spiegelmers which may be used or generated according to the present invention using VEGFR1 as disclosed herein, is based on a similar principle. The manufacture of spiegelmers is described in the international patent application WO 98/08856. Spiegelmers are L-nucleic acids, which means that they are composed of L-nucleotides rather than aptamers which are composed of D-nucleotides as aptamers are. Spiegelmers are characterized by the fact that they have a very high stability in biological system and, comparable to aptamers, specifically interact with the target molecule against which they are directed. In the purpose of generating spiegelmers, a heterogonous population of D-nucleic acids is created and this population is contacted with the optical antipode of the target molecule, in the present case for example with the D-enantiomer of the naturally occurring L-enantiomer of the protein kinase N beta. Subsequently, those D-nucleic acids are separated which do not interact with the optical antipode of the target molecule. However, those D-nucleic acids interacting with the optical antipode of the target molecule are separated, optionally determined and/or sequenced and subsequently the corresponding L-nucleic acids are synthesized based on the nucleic acid sequence information obtained from the D-nucleic acids. These L-nucleic acids which are identical in terms of sequence with the aforementioned D-nucleic acids interacting with the optical antipode of the target molecule, will specifically interact with the naturally occurring target molecule rather than with the optical antipode thereof. Similar to the method for the generation of aptamers it is also possible to repeat the various steps several times and thus to enrich those nucleic acids specifically interacting with the optical antipode of the target molecule.
Ribozymes are catalytically active nucleic acids which preferably consist of RNA which basically comprises two moieties. The first moiety shows a catalytic activity whereas the second moiety is responsible for the specific interaction with the target nucleic acid, in the present case the nucleic acid coding for VEGFR1 as disclosed herein. Upon interaction between the target nucleic acid and the second moiety of the ribozyme, typically by hybridisation and Watson-Crick base pairing of essentially complementary stretches of bases on the two hybridising strands, the catalytically active moiety may become active which means that it catalyses, either intramolecularly or intermolecularly, the target nucleic acid in case the catalytic activity of the ribozyme is a phosphodiesterase activity. Subsequently, there may be a further degradation of the target nucleic acid which in the end results in the degradation of the target nucleic acid as well as the protein derived from the said target nucleic acid due to a lack of newly synthesized VEGFR1 as disclosed herein and a turn-over of prior existing VEGFR1 as disclosed herein. Ribozymes, their use and design principles are known to the one skilled in the art, and, for example described in Doherty and Doudna (Ribozym structures and mechanism. Annu ref Biophys. Biomolstruct. 2001; 30:457-75) and Lewin and Hauswirth (Ribozyme Gene Therapy: Applications for molecular medicine. 2001 7: 221-8).
Antisense oligonucleotides are as such equally known in the art as is their use for the manufacture of a medicament and as a diagnostic agent, respectively. Basically, antisense oligonucleotides hybridise based on base complementarity, with a target RNA, preferably with a mRNA, thereby activate RNase H. RNase H is activated by both phosphodiester and phosphorothioate-coupled DNA. Phosphodiester-coupled DNA, however, is rapidly degraded by cellular nucleases with the exception of phosphorothioate-coupled DNA. These resistant, non-naturally occurring DNA derivatives do not inhibit RNase H upon hybridisation with RNA. In other words, antisense polynucleotides are only effective as DNA RNA hybride complexes. Examples for this kind of antisense oligonucleotides are described, among others, in U.S. Pat. No. 5,849,902 and U.S. Pat. No. 5,989,912. In other words, based on the nucleic acid sequence of the target molecule which in the present case is the nucleic acid coding for VEGFR1 as disclosed herein, either from the target protein from which a respective nucleic acid sequence may in principle be deduced, or by knowing the nucleic acid sequence as such, particularly the mRNA, suitable antisense oligonucleotides may be designed base on the principle of base complementarity.
siRNA is a double stranded RNA having typically a length of about 19 to about 23 nucleotides. The sequence of one of the two RNA strands corresponds to the sequence of the target nucleic acid such as the nucleic acid coding for target molecule, to be degraded. In other words, knowing the nucleic acid sequence of the target molecule, in the present case VEGFR1 in its various forms described herein, preferably the mRNA sequence, a double stranded RNA may be designed with one of the two strands being complementary to said, e.g. mRNA of the target molecule and, upon application of said siRNA to a system containing the gene, genomic DNA, hnRNA or mRNA coding for the target molecule, the respective target nucleic acid will be degraded and thus the level of the respective protein be reduced. The basic principles of designing, constructing and using said siRNA as medicament and diagnostic agent, respectively, is, among others, described in international patent applications WO 00/44895 and WO 01/75164.
Based on the aforementioned design principles, it is possible to generate such siRNA, antisense oligonucleotide and ribozyme, respectively, once the nucleic acid sequence coding for the target molecule is known. This is also true for precursor molecules of nucleic acid such as hnRNA, cDNA and the like, including genomic nucleic acid. Of course, also knowing the respective antisense strand may allow the design of such nucleic acid based compounds given the basic principle of base pair complementarity, preferably based on Watson-Crick base pairing. Accordingly, a further aspect of the present invention is related to specific siRNAs, ribozymes and antisense nucleotides which are directed against or specific for protein kinase N-beta. In the following, this is further illustrated by siRNA, however, this applies to antisense oligonucleotides and ribozymes as well, as will be acknowledged by the ones skilled in the art.
Such siRNA comprises preferably a length of from 15 to 25 nucleotides, whereby this means actually any length comprising 15, 16, 17, 18, 20, 21, 22, 23, 24 or 25 nucleotides. In further embodiments, the siRNA may even exhibit more nucleotides. According the design principles well known in the art, respective siRNA can be generated. Accordingly, the siRNA claimed herein comprises a stretch of preferably any nucleotide length from 15 to 25 consecutive nucleotides which is either at least partially complementary to the sense or to the antisense strand encoding the target molecule, and a second ribonucleotide strand which is at least partially complementary to the first one and thus to the antisense strand and sense strand respectively, encoding the target molecule. Any design principle known in the art of generation or manufacture of siRNA may be applied to this kind of duplex structure. The siRNA space disclosed herein comprises siRNA molecules the antisense strand of which starts with a nucleotides which corresponds to nucleotide no. 1 of a the target molecule as specified above. Further such siRNA molecules start with a nucleotide which corresponds to nucleotide no 2 of the target molecule encoding sequence as specified above, and so on. This kind of scanning over the target molecule encoding sequence is repeated so as to provide all possible siRNA molecules which can be directed against the target molecule. The length of any of the siRNA molecules thus generated may be any length suitable for siRNA, more particularly any length as specified above. Preferably, the various siRNA molecule of the siRNA molecule space disclosed herein, overlap except the most 5′ terminal nucleotide of the antisense strand or sense strand. It is obvious that the thus obtained antisense sequences have to complemented through base pairing so as to form the at least partially double-stranded structure required for a functionally active siRNA.
MicroRNA for use in therapeutic applications are, for example, described in Soifer H S et al. (Soifer H S et al., Molecular therapy, vol. 15, no. 12, December 2007, pages 2070-2079).
Antagomirs for use in therapeutic applications are, for example, described in Stenvang J & Kauppinen S (Stenvang J & Kauppinen S, Expert Opin. Biol. Ther. (2008) 8(1), pages 59-81).
A preferred embodiment the PKN3 inhibitor is an siRNA which is double-stranded (ds 23 mer) having the following composition and structure, respectively:









(SEQ ID NO: 11)



5′ 5u8u7c6g8a6g5c7u7a6g5c5 3′



 



(SEQ ID NO: 12)



3′ a6c6g8u7c5u7a8g6g5u7a8a 5′






with unmodified ribonucleotides being as indicated and modified ribonucleotides being represented as follows:

5: 2′-O-Methyl-u,
6: 2′-O-Methyl-a,
7: 2′-O-Methyl-c,
8: 2′-O-Methyl-g.

    
    
        In a further preferred embodiment of the various aspects of the present invention the PKN3 inhibitor is a composition referred to in the prior art and herein as Atu027. The active pharmaceutical ingredient (API) of Atu027 is a PKN3-specific siRNA. The siRNA is a double stranded RNA molecule containing naturally occurring 2′-O-Methyl-modifications. The 2′-O-methyl modifications stabilize the RNA by protection from nuclease attack. The double strand (ds-23 mer) is composed of the following sequences:
    
    











(SEQ ID NO: 11)



5′ 5u8u7c6g8a6g5c7u7a6g5c5 3′



 



(SEQ ID NO: 12)



3′ a6c6g8u7c5u7a8g6g5u7a8a 5′






with unmodified ribonucleotides being as indicated and modified ribonucleotides being represented as follows:

5: 2′-O-Methyl-u,
6: 2′-O-Methyl-a,
7: 2′-O-Methyl-c,
8: 2′-O-Methyl-g.
For production of Atu027 the PKN3-specific siRNA is formulated with positively charged liposomes composed of three lipids, i.e. the cationic AtuFect01, the neutral, fusogenic DPyPE helperlipid and the PEGylated lipid MPEG-2000-DSPE in a molar ratio of 50/49/1 to deliver the negatively charged siRNA in lipoplexed form. AtuFect01 and DPyPE helperlipid are novel excipients. The third lipid MPEG-2000-DSPE is a known excipient. The structure of the 3 lipids is presented below:
Cationic lipid AtuFect01: ((β-(L-Arginyl)-2,3-L-diaminopropionic acid-N-palmityl-N-oleyl-amide tri-hydrochloride)




Fusogenic/helperlipid DPyPE: 1,2-Diphytanoyl-sn-glycero-3-phosphoethanolamine





PEG-lipid MPEG-2000-DSPE: N-(Carbonyl-methoxypolyethyleneglycol-2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine sodium salt





It is within the present invention that any of the PKN3 inhibitors disclosed herein can be used in connection with each and any aspect of the present invention, including the method of the present invention and the PKN3 inhibitor for use in a method for the treatment of a subject suffering from or being at risk of suffering from a disease of the present invention.
It is within the present invention that any of the disease disclosed herein can be used in connection with each and any aspect of the present invention, including the method of the present invention and the PKN3 inhibitor for use in a method for the treatment of a subject suffering from or being at risk of suffering from a disease of the present invention.
It is also within the present invention that any of the VEGFR1 and nucleic acid coding therefor disclosed herein can be used in connection with each and any aspect of the present invention, including the method of the present invention and the PKN3 inhibitor for use in a method for the treatment of a subject suffering from or being at risk of suffering from a disease of the present invention.
Methods for the detection of VEGFR1 are known in the art and include, but are not limited to anti-VEGFR1 antibodies. In embodiments of the various aspects of the present invention VEGFR1 is detected by means of ELISA. However, other means are known to a person skilled in the art such as detection by mass spectrometry and the like.
In connection with the various aspects of the present invention a sample is a sample of a body fluid, whereby the body fluid is selected from the group comprising blood, plasma, liquor, urine and saliva. Preferred samples are blood samples and plasma samples.
Methods for the detection of a nucleic acid coding for VEGFR1 are also known in the art and include, but are not limited to PCR and RT-PCR.
VEGFR1 and soluble VEGFR1 (sVEGFR1) are known in the art and described, among others, in Caine G J et al. (Caine, G J, European Journal of Clinical Investigation (2003), 33, 883-890) or Barleon B et al. (Barleon B et al., Angionesis 4: 143-154 (2001)). Barleaon B et al. (supra) also disclose that the titre of soluble VEGFR1 is about 160 pg/ml in healthy volunteers.
The present invention is now further illustrated by the attached Figs and examples from which further feature, embodiments and advantages of the present invention may be taken.
The following list summarizes some of the SEQ ID NOs and provide an indication as to what they represent.













SEQ ID NO: 1
amino acid sequence of soluble VEGFR1 or VEGFR1



variant 2


SEQ ID NO: 2
nucleotide sequence coding for soluble VEGFR1 or



VEGFR1 transcript variant 2


SEQ ID NO: 3
amino acid sequence of VEGFR1 variant 1


SEQ ID NO: 4
nucleotide sequence coding for VEGFR1 transcript



variant 1


SEQ ID NO: 5
amino acid sequence of VEGFR1 variant 3


SEQ ID NO: 6
nucleotide sequence coding for VEGFR1 transcript



variant 3


SEQ ID NO: 7
amino acid sequence of VEGFR1 variant 4


SEQ ID NO: 8
nucleotide sequence coding for VEGFR1 transcript



variant 4


SEQ ID NO: 9
amino acid sequence of PKN3


SEQ ID NO: 10
nucleotide sequence coding for PKN3












BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a diagram indicating PKN3 knock down, VEGFR1 expression and VEGFR2 expression in PC-3 cells. Human PC-3 cell line was obtained from American Type Culture Collection and cultivated according to the ATCC's recommendation. Cell line was transfected with Luciferase AtuPLEX and Atu027, respectively. Briefly, about 16 h after cell seeding siRNA-lipoplex solution diluted in 10% serum containing medium was added to the cells to achieve transfection concentration of 20 nM siRNA. After transfection (24 h, 48 h, 72 h, and 96 h), cells were lysed, total RNA was isolated and subjected to qRT-PCR. Graphs show respective mRNA level as mean of technical replicate relative to untreated @ 24 h. A decrease in VEGFR1 but not VEGFR2 expression in response to PKN3 knock down is observed.
FIG. 2 is a diagram indicating PKN3 knock down, VEGFR1 expression and VEGFR2 expression in MDA-MB-435 cells. Human MDA-MB-435 cell line was obtained from American Type Culture Collection and cultivated according to the ATCC's recommendation. Cell line was transfected with Luciferase AtuPLEX and Atu027, respectively. Briefly, about 16 h after cell seeding siRNA-lipoplex solution diluted in 10% serum containing medium was added to the cells to achieve transfection concentration of 20 nM siRNA. After transfection (24 h, 48 h, 72 h, and 96 h), cells were lysed, total RNA was isolated and subjected to qRT-PCR. Graphs show respective mRNA level as mean of technical replicate relative to untreated @ 24 h. A decrease in VEGFR1 but not VEGFR2 expression in response to PKN3 knock down is observed.
FIG. 3 is a diagram indicating PKN3 knock down, VEGFR1 expression and VEGFR2 expression in SKBR3 cells. Human SKBR3 cell line was obtained from American Type Culture Collection and cultivated according to the ATCC's recommendation. Cell line was transfected with Luciferase AtuPLEX and Atu027, respectively. Briefly, about 12 h after cell seeding siRNA-lipoplex solution diluted in 10% serum containing medium was added to the cells to achieve transfection concentration of 20 nM siRNA. After transfection (24 h, 48 h, 72 h, and 96 h), cells were lysed, total RNA was isolated and subjected to qRT-PCR. Graphs show respective mRNA level as mean of technical replicate relative to untreated @24 h. A decrease in VEGFR1 but not VEGFR2 expression in response to PKN3 knock down is observed.
FIG. 4 is a representation of the design of a clinical phase I study. Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn for biomarker analysis.
FIG. 5 shows the result of a biomarker analysis in plasma from humans treated with Atu027. Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn from 9 patients and plasma was prepared. Samples were analyzed for biomarker analyte concentration. In the graph the ratio of post/pre treatment plasma level is shown for the VEGF isoforms and their receptors.
FIG. 6 shows the result of a biomarker analysis in plasma from humans treated with Atu027: single analytes—VEGF. Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn from 9 patients and plasma was prepared. Samples were analyzed for biomarker analyte concentration. In the graph the absolute values for VEGF are presented.
FIG. 7 shows the result of a biomarker analysis in plasma from humans treated with Atu027: single analytes—VEGF-B. Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn from 9 patients and plasma was prepared. Samples were analyzed for biomarker analyte concentration. In the graph the absolute values for VEGF-B are presented.
FIG. 8 shows the result of a biomarker analysis in plasma from humans treated with Atu027: single analytes—VEGF-C. Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn from 9 patients and plasma was prepared. Samples were analyzed for biomarker analyte concentration. In the graph the absolute values for VEGF-C are presented.
FIG. 9 shows the result of a biomarker analysis in plasma from humans treated with Atu027: single analytes—VEGF-D. Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn from 9 patients and plasma was prepared. Samples were analyzed for biomarker analyte concentration. In the graph the absolute values for VEGF-D are presented.
FIG. 10 shows the result of a biomarker analysis in plasma from humans treated with Atu027: single analytes—VEGFR1 (which is also referred to as VEGFR-1). Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn from 9 patients and plasma was prepared. Samples were analyzed for biomarker analyte concentration. In the graph the absolute values for VEGFR-1 are presented. In 7 out of 9 patient samples, VEGFR-1 was decreased after repeated Atu027 treatment.
FIG. 11 shows the result of a biomarker analysis in plasma from humans treated with Atu027: single analytes—VEGFR2 (which is also referred to as VEGFR-2). Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn from 9 patients and plasma was prepared. Samples were analyzed for biomarker analyte concentration. In the graph the absolute values for VEGFR-2 is presented.
FIG. 12 shows the result of a biomarker analysis in plasma from humans treated with Atu027: single analytes—VEGFR3 (which is also referred to as VEGFR-3). Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn from 9 patients and plasma was prepared. Samples were analyzed for biomarker analyte concentration. In the graph the absolute values for VEGFR-3 is presented.
FIG. 13 represents SEQ ID NO: 1.
FIG. 14 represents SEQ ID NO: 2.
FIG. 15 represents SEQ ID NO: 3.
FIG. 16 represents SEQ ID NO: 4.
FIG. 17 represents SEQ ID NO: 5.
FIG. 18 represents SEQ ID NO: 6.
FIG. 19 represents SEQ ID NO: 7.
FIG. 20 represents SEQ ID NO: 8.
FIG. 21 represents SEQ ID NO: 9.
FIG. 22 represents SEQ ID NO: 10.



EXAMPLES
Example 1
Synthesis of RNAi Molecule (AtuRNAi) for In Vitro Studies
The siRNA molecules (AtuRNAi) of this invention are described in Table 1. These molecules were synthesized by BioSpring GmbH (Frankfurt a. M., Germany).









TABLE 1





siRNA name
sequence 5′ to 3′
SEQ ID NO







PKN3 s
agacuugaggacuuccuggacaa
13


 


PKN3 as
uuguccaggaaguccucaagucu
14


 


Luciferase s
aucacguacgcggaauacuucga
15


 


Luciferase as
ucgaaguauuccgcguacgugau
16









Nucleotides with 2′-O-methyl modifications are underlined; “s” stands for the sense strand; and “as” stands for the antisense strand.
The duplexes formed by “PKN3 as” and “PKN3 s”, and formed by “Luciferase as” and “Luciferase s” lack 3′-overhangs and are chemically stabilized by alternating 2′-O-methyl sugar modifications on both strands, whereby unmodified nucleotides face modified ones on the opposite strand (Table 1). These duplexes are also referred to herein as PKN3 and Luciferase and were resolved in water to obtain a stock concentration of 1 μM.
Example 2
Formulation of the AtuPLEX
The AtuPLEX formulation was prepared as essentially described in Santel et al. (Santel et al. Gene Therapy (2006) 13, 1222-1234). Cationic liposomes comprising the novel cationic lipid AtuFECT01 ((β-L-arginyl-2,3-L-diaminopropionic acid-N-palmityl-N-oleyl-amide trihydrochloride), the neutral phospholipid 1,2-diphytanoyl-sn-glycero-3-phosphoethanolamine (DPyPE) and the PEGylated lipid N-(Carbonyl-methoxypolyethyleneglycol-2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine sodium salt (DSPE-PEG) in a molar ratio of 50/49/1 were prepared by lipid film re-hydration in 270 mM sterile RNase-free sucrose solution to a total lipid concentration of 4.335 mg/ml. Subsequently, the multilamellar dispersion was further processed by high-pressure homogenization using an EmulsiFlex C3 device (Avestin, Inc., Ottawa, Canada).
To generate siRNA-lipoplexes (AtuPLEX), the obtained liposomal dispersion was mixed with an equal volume of a 0.5625 mg/ml solution of siRNA in 270 mM sucrose, resulting in a calculated charge ratio of nucleic acid backbone phosphates to cationic lipid nitrogen atoms of approximately 1:4. The size of the liposome and the lipoplex dispersion and the zeta potential were measured using a Zetasizer Nano-ZS (Malvern Instruments, Worcestershire, UK).
The active pharmaceutical ingredient (API) of Atu027 is the PKN3-siRNA. The siRNA is a double stranded RNA molecule containing naturally occurring 2′-O-Methyl-modifications. The 2′-O-methyl modifications stabilize the RNA by protection from nuclease attack.
The double strand (ds-23 mer) is composed of the following sequence:









(SEQ ID NO: 11)



5′ 5u8u7c6g8a6g5c7u7a6g5c5 3′



 



(SEQ ID NO: 12)



3′ a6c6g8u7c5u7a8g6g5u7a8a 5′






Unmodified ribonucleotides: x;

Modifications: 5: 2′-O-Methyl-u, 6: 2′-O-Methyl-a, 7: 2′-O-Methyl-c, 8: 2′-O-Methyl-g.

For Atu027 production PKN3-siRNA is formulated with positively charged liposomes composed of three lipids, i.e. the cationic AtuFect01, the neutral, fusogenic DPyPE helperlipid and the PEGylated lipid MPEG-2000-DSPE in a molar ratio of 50/49/1 to deliver the negatively charged siRNA in lipoplexed form. AtuFect01 and DPyPE helperlipid are novel excipients. The third lipid MPEG-2000-DSPE is a known excipient. The structure of the 3 lipids is presented below:
Cationic lipid AtuFect01: ((β-(L-arginyl)-2,3-L-diaminopropionic acid-N-palmityl-N-oleyl-amide tri-hydrochloride)




Fusogenic/helperlipid DPyPE: 1,2-Diphytanoyl-sn-Glycero-3-Phosphoethanolamine





PEG-lipid MPEG-2000-DSPE: N-(Carbonyl-methoxypolyethyleneglycol-2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine sodium salt





Example 3
Expression of VEGFR-1 in Response to In Vitro Gene Silencing of Human PKN3 in Human Prostate Cancer PC-3 Cells
3×105 PC-3 cells were plated in 10-cm dishes, transfected 16 h later with 20 nM of the siRNA as described in Example 1 and 1 μg/ml liposome were prepared as described in Example 2, whereby the liposome consisted of the cationic lipid β-(L-arginyl)-2,3-L-diaminopropionic acid-N-palmityl-N-oleyl-amide tri-hydrochloride (AtuFECT01), the fusogenic lipid 1,2-diphytanoyl-sn-glycero-3-phosphoethanolamine (DPyPE) and the PEGylated lipid MPEG-2000-DSPE in a molar ratio of 50/49/1. Cells were lysed for RNA extraction 24 h, 48 h, 72 h and 96 h after transfection, respectively.
Total RNA was prepared with the InviTrap® Spin Cell RNA Mini Kit (Invitek, Berlin, Germany). Inhibition of PKN3 mRNA expression, expression of VEGFR1 and VEGFR2 mRNA was detected by real time RT-PCR (TaqMan) analysis using 300 nM PKN3, VEGFR1 and VEGFR2 specific forward and reverse primer and 100 nM probe. The sequences of the primers in TaqMan are listed in the following table, whereby UPR means upper primer, LWR means lower primer, and PRB means probe.










TABLE 2





Name
Primer/Probe
Sequence 5′ to 3′
SEQ ID NO







Human
UPR
CACTTTGGGAAGGTCCTCCTG
17


PKN3
PRB
FAM-





TTCAAGGGGACAGGGAAATACTACGCCA-
18




BHQ1




LWR
CCTCCTGCTTCTTCAGTGCTTT
19


 


Human
UPR
CCCCGATTATGTGAGAAAAGGA
20


VEGFR1
PRB
FAM-CGACTTCCTCTGAAATGGATGGCTCCTG-
21




BHQ1




LWR
CGCTCTTGGTGCTGTAGATTTTG
22


 


Human
UPR
TCTGCCTACCTCACCTGTTTCC
23


VEGFR2
PRB
FAM-
24




ATGGAGGAGGAGGAAGTATGTGACCCCA-





TAMRA




LWR
TGACTGATTCCTGCTGTGTTGTC
25









The reaction was carried out in 25 μl and assayed on the StepOnePlusTM Real-Time PCR System (Applied Biosystems) according to the manufacturer's instructions under the following conditions: 48° C. for 30 min, 95° C. for 10 min, followed by 40 cycles of 15 s at 95° C. and 1 min at 60° C. mRNA amounts are shown relative to untreated control lysed 24 h after transfection.
The results are shown in FIG. 1 indicating in vitro a marked decrease in VEGFR1 but not VEGFR2 mRNA expression in response to PKN3 knock down 72 h and 96 h post-transfection in human prostate cancer PC-3 cells.
Example 4
Expression of VEGFR-1 in Response to In Vitro Gene Silencing of Human PKN3 in Human Breast Carcinoma MDA-MB-435 Cells
3×105 MDA-MB-435 cells were plated in 10-cm dishes, transfected 16 h later with 20 nM of the siRNA as described in Example 1 and 1 μg/ml liposome were prepared as described in Example 2, whereby the liposome consisted of the cationic lipid β-(L-arginyl)-2,3-L-diaminopropionic acid-N-palmityl-N-oleyl-amide tri-hydrochloride (AtuFECT01), the fusogenic lipid 1,2-diphytanoyl-sn-glycero-3-phosphoethanolamine (DPyPE) and the PEGylated lipid MPEG-2000-DSPE in a molar ratio of 50/49/1. Cells were lysed for RNA extraction 24 h, 48 h, 72 h and 96 h after transfection, respectively.
Total RNA was prepared with the InviTrap® Spin Cell RNA Mini Kit (Invitek, Berlin, Germany). Inhibition of PKN3 mRNA expression, expression of VEGFR1 and VEGFR2 mRNA was detected by real time RT-PCR (TaqMan) analysis as described in example 3. mRNA amounts are shown relative to untreated control lysed 24 h after transfection.
The results are shown in FIG. 2 indicating in vitro a marked decrease in VEGFR1 but not VEGFR2 mRNA expression in response to PKN3 knock down at all time-points analyzed (24 h, 48 h, 72 h and 96 h post-transfection) in human breast carcinoma MDA-MB-435 cells.
Example 5
Expression of VEGFR-1 in Response to In Vitro Gene Silencing of Human PKN3 in Human Ovarian Cancer SKBR3 Cells
3×105 SKBR3 cells were plated in 10-cm dishes, transfected 16 h later with 20 nM of the siRNA as described in Example 1 and 1 μg/ml liposome were prepared as described in Example 2, whereby the liposome consisted of the cationic lipid β-(L-arginyl)-2,3-L-diaminopropionic acid-N-palmityl-N-oleyl-amide tri-hydrochloride (AtuFECT01), the fusogenic lipid 1,2-diphytanoyl-sn-glycero-3-phosphoethanolamine (DPyPE) and the PEGylated lipid MPEG-2000-DSPE in a molar ratio of 50/49/1. Cells were lysed for RNA extraction 24 h, 48 h and 72 h after transfection, respectively.
Total RNA was prepared with the InviTrap® Spin Cell RNA Mini Kit (Invitek, Berlin, Germany). Inhibition of PKN3 mRNA expression, expression of VEGFR1 and VEGFR2 mRNA was detected by real time RT-PCR (TaqMan) analysis as described in example 3. mRNA amounts are shown relative to untreated control lysed 24 h after transfection.
The results are shown in FIG. 3 indicating in vitro a marked decrease in VEGFR1 but not VEGFR2 mRNA expression in response to PKN3 knock down 72 h post-transfection in human ovarian cancer SKBR3 cells.
Example 6
Design of Clinical Phase I Study with Atu027
The Phase I study with Atu027 “A prospective, open label, single-centre, dose finding phase I study with Atu027 (an siRNA formulation) in subjects with advanced solid cancer—Atu027-I-01” (EudraCT No. 2008-005588-32/NCT00938574) was conducted. Study design is shown in FIG. 4. Before (0 h) and 24 h after the last (24 h) repeated 4-h intravenous infusion treatment with Atu027 blood was withdrawn for biomarker analysis. EDTA plasma was prepared by centrifugation according to standard protocols and stored at −20° C.
Example 7
Biomarker Analysis in Plasma of Humans Treated with Atu027
Before (0 h) and 24 h after the last (24 h) repeated treatment with Atu027 blood was withdrawn from nine patients and EDTA plasma was prepared. Samples were analyzed in a multiplexed immunoassay for concentration of respective analytes using the Luminex technology.
In FIG. 5 the ratio of post/pre treatment plasma level (24 h level divided by the 0 h value) in the individual patient is shown for the VEGF isoforms VEGF, VEGF-B, VEGF-C, VEGF-D and their receptors VEGFR1, VEGFR2 and VEGFR3. The Atu027 doses based on the siRNA content are given in the right table. In seven out of nine patients VEGFR1 level were markedly decreased after Atu027 treatment.
In addition to the Atu027 doses indicated in FIG. 5 doses of 0.036 mg/kg Atu027 (based on siRNA content) were administered to three patients whereby two patients showed a marked decrease in the ratio of soluble FLT-1 (sFLT-1) post/pretreatment.
The absolute plasma level of the single analytes VEGF, VEGF-B, VEGF-C, VEGF-D, VEGFR1, VEGFR2 and VEGFR3 are shown in graphs and tables in FIG. 6, FIG. 7, FIG. 8, FIG. 9, FIG. 10, FIG. 11 and FIG. 12. Again, a marked decrease of VEGFR1 concentration after treatment could be detected (FIG. 10) whereas the VEGF, VEGF-B, VEGF-C, VEGF-D, VEGFR2 and VEGFR3 level remained unchanged in most patients and slightly increased or decreased in single individuals.
The features of the present invention disclosed in the specification, the claims and/or the drawings may both separately and in any combination thereof be material for realizing the invention in various forms thereof.

## Claims

1. A method of treating a subject and determining the responsiveness of the subject to treatment with a protein kinase N beta (PKN3) inhibitor comprising:
determining the level of a VEGFR1 or of a nucleic acid coding for a VEGFR1 in a sample from the subject prior to the treatment of said subject,
administering a PKN3 inhibitor to said subject having a disease treatable with said PKN3 inhibitor;
determining the level of a VEGFR1 or of a nucleic acid coding for a VEGFR1 in a sample from the subject after the subject has been subjected to the method of treatment; and
identifying the subject as a responder to said treatment with said PKN3 inhibitor if the level of a VEGFR1 or a nucleic acid coding for a VEGFR1 in a sample from the subject after the subject having been subjected to the method of treatment is decreased compared to the level of a VEGFR1 or a nucleic acid coding for a VEGFR1 in a sample from the subject prior to the subject having being subjected to the method of treatment; and
administering said PKN3 inhibitor to a subject identified as a responder to said treatment.

2. The method according to claim 1, wherein the decrease in level of the VEGFR1 or the nucleic acid coding for the VEGFR1 is a decrease of 10% or more, of 20% or more, 40% or more, 60% or more or 80% or more.

3. The method according to claim 1, wherein the VEGFR1 is VEGFR1, VEGFR1 variant 2, VEGFR1 variant 1, VEGFR1 variant 3, VEGFR1 variant 4, soluble VEGFR1, or soluble VEGFR1 variant 2 or is a nucleic acid encoding VEGFR1, VEGFR1 variant 2, VEGFR1 variant 1, VEGFR1 variant 3, VEGFR1 variant 4, soluble VEGFR1, or soluble VEGFR1 variant 2.

4. The method according to claim 1, wherein the PKN3 inhibitor is an siRNA as follows:









(SEQ ID NO: 11)



5′ 5u8u7c6g8a6g5c7u7a6g5c5 3′



 



(SEQ ID NO: 12)



3′ a6c6g8u7c5u7a8g6g5u7a8a 5′





with unmodified ribonucleotides being as indicated and modified ribonucleotides being represented as follows:
5: 2′-O-Methyl-u,
6: 2′-O-Methyl-a,
7: 2′-O-Methyl-c,
8: 2′-O-Methyl-g.