(12) Patent Application Publication (10) Pub. No.: US 2012/0264.634 A1 Amersdorfer Et Al
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US 20120264.634A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0264.634 A1 Amersdorfer et al. (43) Pub. Date: Oct. 18, 2012 (54) MARKER SEQUENCES FOR PANCREATIC Publication Classification CANCER DISEASES, PANCREATIC (51) Int. Cl. CARCINOMIA AND USE THEREOF C40B 30/04 (2006.01) GOIN 2L/64 (2006.01) (75) Inventors: Peter Amersdorfer, Graz (AT); GOIN 27/72 (2006.01) Annabel Höpfner, Dortmund (DE); C07K I4/435 (2006.01) Angelika Lueking, Bochum (DE) C40B 40/06 (2006.01) C40B 40/10 (2006.01) CI2N 5/09 (2010.01) (73) Assignee: PROTAGEN Aktiengesellschaft, C7H 2L/04 (2006.01) Dortmund (DE) GOIN 33/574 (2006.01) GOIN 27/62 (2006.01) (21) Appl. No.: 13/498,964 (52) U.S. Cl. ........... 506/9:436/501; 435/6.14; 435/7.92; 506/16:506/18: 435/2:536/23.1; 530/350 (22) PCT Filed: Sep. 29, 2010 (57) ABSTRACT The present invention relates to novel marker sequences for (86). PCT No.: PCT/EP2010/064510 pancreatic cancer diseases, pancreatic carcinoma and the diagnostic use thereof together with a method for Screening of S371 (c)(1), potential active Substances for pancreatic cancer diseases, (2), (4) Date: Jun. 22, 2012 pancreatic carcinoma by means of these marker sequences. Furthermore, the invention relates to a diagnostic device con (30) Foreign Application Priority Data taining Such marker sequences for pancreatic cancer diseases, pancreatic carcinoma, in particular a protein biochip and the Sep. 29, 2009 (EP) .................................. O9171690.2 use thereof. Patent Application Publication Oct. 18, 2012 US 2012/0264.634 A1 US 2012/0264.634 A1 Oct. 18, 2012 MARKER SEQUENCES FOR PANCREATIC Doucette-Stamm, L., Hill, D. E. and Vidal, M. (2003) C. CANCER DISEASES, PANCREATIC elegans ORFeome Version 1.1 : experimental verification of CARCINOMIA AND USE THEREOF the genome annotation and resource for proteome-scale pro tein expression. Nat Genet, 34, 35-41.; Walhout, A. J., Temple, G. F., Brasch, M.A., Hartley, J. L., Lorson, M.A., 0001. The present invention relates to novel marker van den Heuvel, S. and Vidal, M. (2000) GATEWAY recom sequences for pancreatic cancer diseases, pancreatic carci binational cloning: application to the cloning of large num noma, and the diagnostic use thereof together with a method bers of open reading frames or ORFeomes. Methods Enzy for screening potential active Substances for pancreatic can mol, 328, 575-592). However, an approach of this type is cer diseases of this type by means of these marker sequences. strongly connected to the progress of the genome sequencing Furthermore, the invention relates to a diagnostic device con projects and the annotation of these gene sequences. Further taining marker sequences of this type for pancreatic cancer more, the determination of the expressed sequence can be diseases, pancreatic carcinoma, in particular aprotein biochip ambiguous due to differential splicing processes. This prob and the use thereof lem may be circumvented by the application of cDNA expres 0002 The 5-year-survival rate for pancreatic carcinoma of sion libraries (Büssow, K., Cahill, D., Nietfeld, W., Bancroft, approx. 1% is the lowest of all cancertypes (Parkin, D. M., F. D., Scherzinger, E., Lehrach, H. and Walter, G. (1998) A Bray, et al. (2001). “Estimating the world cancer burden: method for global protein expression and antibody Screening Globocan 2000.” Int J Cancer 94(2): 153-6). Early diagnosis on high-density filters of an arrayed cDNA library. Nucleic might increase the 5-year survival rate to 40% (Yeo, C.J. and Acids Research, 26, 5007-5008; Bissow, K., Nordhoff, E., J. L. Cameron (1998). “Prognostic factors in ductal pancre Lübbert, C, Lehrach, H. and Walter, G. (2000) A human atic cancer. Langenbecks Arch Surg. 383 (2): 129-33). There cDNA library for high-throughput protein expression screen fore, for diagnosis, the precursor diseases of pancreatic can ing. Genomics, 65, 1-8; Holz, C. Lueking, A., Bovekamp, L., cer need to be considered as well, such as PDAC (pancreatic Gutjahr, C, Bolotina, N., Lehrach, H. and Cahill, D.J. (2001) ductal adenocarcinoma), PanN (pancreatic intraepithelial A human clNA expression library in yeast enriched for open neoplasias), pancreatic lesions, CP (chronic pancreatitis), reading frames. Genome Res, 11, 1730-1735; Lueking, A., including endocrine tumors of the pancreas. Especially Holz, C, Gotthold, C, Lehrach, H. and Cahill, D. (2000) A PanID are associated with pancreatic lesions and differentiate system for dual protein expression in Pichia pastoris and them morphologically into Pan In 1A, 1B, 2, and 3 (Kern, S., Escherichia coli, Protein Expr: Purif., 20, 372-378). The R. Hruban, et al. (2001). “A white paper: the product of a cDNA of a particular tissue is hereby cloned into a bacterial or pancreas cancer think tank. Cancer Res 61 (12): 4923-32). an eukaryotic expression vector, Such as, e.g., yeast. The Pancreatic lesions have also been described for CP. Endocrine vectors used for the expression are generally characterized in (benign or malignant) tumors of the pancreas, particularly that they carry inducible promoters that may be used to con neuroendocrine tumors, are relevant as well. trol the time of protein expression. Furthermore, expression 0003 WO2008.064670 describes e.g. marker genes for vectors have sequences for so-called affinity epitopes or affin pancreas obtained by means of proteome analysis and histo ity proteins, which on the one hand permit the specific detec logical investigations. tion of the recombinant fusion proteins by means of an anti 0004 Protein biochips are gaining increasing industrial body directed against the affinity epitope, and on the other importance in analysis and diagnosis as well as in pharma hand the specific purification via affinity chromatography ceutical development. Protein biochips have become estab (IMAC) is rendered possible. lished as screening instruments. 0006 For example, the gene products of a cDNA expres 0005. The rapid and highly parallel detection of a multi sion library from human fetal brain tissue in the bacterial plicity of specifically binding analysis molecules in a single expression system Escherichia coli were arranged in high experiment is rendered possible hereby. To produce protein density format on a membrane and could be successfully biochips, it is necessary to have the required proteins avail screened with different antibodies. It was possible to show able. For this purpose, in particular protein expression librar that the proportion of full-length proteins is at least 66%. ies have become established. The high throughput cloning of Additionally, the recombinant proteins from the library could defined open reading frames is one possibility (Heyman, J.A., be expressed and purified in a high-throughput manner Cornthwaite, J., Foncerrada, L., Gilmore, J. R. Gontang, E., (Braun P. Hu, Y. Shen, B., Halleck, A., Koundinya, M., Hartman, K.J., Hernandez, C. L., Hood, R., Hull, H.M., Lee, Harlow, E. and LaBaer, J. (2002) Proteome-scale purification W.Y., Marcil, R., Marsh, E. J., Mudd, K. M., Patino, M.J., of human proteins from bacteria. Proc Natl AcadSci USA, 99, Purcell, T.J., Rowland, J.J., Sindici, M. L. and Hoeffler, J.P., 2654-2659; Büssow (2000) supra; Lueking, A., Horn, M., (1999) Genome-scale cloning and expression of individual Eickhoff, H., Büssow, K., Lehrach, H. and Walter, G. (1999) open reading frames using topoisomerase I-mediated liga Protein microarrays for gene expression and antibody Screen tion. Genome Res, 9, 383-392: Kersten, B., Feilner, T., ing. Analytical Biochemistry, 270, 103-111). Protein biochips Kramer, A., Wehrmeyer, S. Possling, A. Witt, I., Zanor, M.I., of this type based on cDNA expression libraries are in par Stracke, R., Lueking, A., Kreutzberger, J., Lehrach, H. and ticular the subject matter of WO99/57311 and WO99/57312. Cahill, D.J. (2003) Generation of Arabidopsis protein chip 0007 Furthermore, in addition to antigen-presenting pro for antibody and serum screening. Plant Molecular Biology, tein biochips, antibody-presenting arrangements are likewise 52, 999-1010; Reboul, J., Reboul, J., Vaglio, P., Rual, J. F., described (Lal et al (2002) Antibody arrays: An embryonic Lamesch, P., Martinez, M., Armstrong, C.M., Li, S., Jacotot, but rapidly growing technology, DDT, 7, 143-149; Kusnezow L., Bertin, N., Janky, R., Moore, T., Hudson, J.R., Jr., Hartley, etal. (2003), Antibody microarrays: An evaluation of produc J. L., Brasch, M.A., Vandenhaute, J., Boulton, S., Endress, G. tion parameters, Proteomics, 3, 254-264). A., Jenna, S., Chevet, E., Papasotiropoulos, V., Tolias, P. P. O008) Protein-biochips have a advantageously high sensi Ptacek, J., Snyder, M., Huang, R., Chance, M. R. Lee, H., tivity. US 2012/0264.634 A1 Oct. 18, 2012 0009. However, there is a great need to provide indication tion of the body fluid or tissue extract with the marker specific diagnostic devices, such as a protein biochip. sequences from a.) is carried out. 0010. The object of the present invention is therefore to 0021. The invention therefore likewise relates to diagnos provide improved marker sequences and the diagnostic use tic agents for the diagnosis of pancreatic cancer diseases up to thereof for the treatment of pancreatic cancer diseases up to pancreatic carcinoma respectively selected from the group pancreatic carcinoma. SEQ 1-1004, preferably SEQ 503-1004, or respectively a 0011. The object of the present invention is solved in pro protein coding therefor or respectively a partial sequence or viding of novel marker sequences SEQ 1-1004, which are fragment thereof identified for the first time by means of a protein biochip, in 0022. The detection of an interaction of this type can be particular including bioinformatic analysis. Therefore, SEQ carried out, for example, by a probe, in particular by an 1-1004 are identified for the first time by means of a protein antibody. biochip. 0023 The invention therefore likewise relates to the object 0012.