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(12) Patent Application Publication (10) Pub. No.: US 2004/0191783 A1 Leclercq Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2004/0191783 A1 Leclercq Et Al US 20040191783A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2004/0191783 A1 Leclercq et al. (43) Pub. Date: Sep. 30, 2004 (54) LOW DENSITY MICRO-ARRAY ANALYSIS Publication Classification IN HUMAN BREAST CANCER (51) Int. Cl." .............................. C12O 1/68; C12M 1/34 (76) Inventors: Guy Leclercq, Bruxelles (BE); Jose (52) U.S. Cl. ............................................. 435/6; 435/287.2 Remacle, Malonne (BE); Marc Lacroix, Baelen (BE); Nathalie (57) ABSTRACT Zammatteo, Gelbressee (BE); Francoise de Longueville, Natoye (BE) A method and kit comprising reagents for detection and/or Correspondence Address: quantification of polynucleotide or polypeptide Sequences Bell, Boyd & Lloyd, LLC potentially present in a Sample, Said Sequences representing P.O. BOX 1135 the gene expression associated with different cell pheno Chicago, IL 60690-1135 (US) types and functions and differentiating the gene expressed in cancer tissue compared to normal or reference material. The (21) Appl. No.: 10/404,743 method and kit are especially Suited for the identification and/or characterization of cancertissues and for follow up of (22) Filed: Mar. 31, 2003 patient treatments. Patent Application Publication Sep. 30, 2004 Sheet 1 of 6 US 2004/0191783 A1 Figure 1 Presentation of the pattern of the microarray for gene expression analysis of breast cancer with the appropriated controls =Positive Hybridization Control -Negative Hybridization Control 8 =Negative Detection Control -Housekeeping gene OO =Internal Standard O O (3) (S) () O Conc curve -t-Detection OOOOOOOOO GOOOOOOOOOOOOOOOOO OOOO (). OOOO OOOO (). OOOO OOOO (). OOOO O (). OOOOOOO O (). OOOOOOOO (). OOOOOOO OOOOOOO O OOOOOOOOOOOOOOO (SO OOOO (). OOOO OOOO (OOOOOOOO () O OOO OOOOOOOOO OOOOOOOOO OOOOOOOOO OOOOOOO () () OOOOOOO () O OOOOOOO () () OOOOOOOOO OOOOOOOOOOOOOOOOOO OOOO (). OOOO OOOO (). OOOO OOOO (). OOOO OOOOOOO () O OOOOOOO () O (OOOOOOO (OO O (). OOOOOOO O (OOOOOOOOO (). OOOOOOO OOOOOOOOO OOOOOOOOOOOOOOOOOO O OOO () O OOO OOOO () O O O O OOOO (). OOOO O (). OOOOOOO O (). OOOOOOO O (). OOOOOOO OOOOOOOOO OOOOOOOOOOOOOOOOOO OOOO (). OOOO OOOO (). OOOOOOOO () O OOO . O (9 OOOOOOO O (). OOOOOOO Patent Application Publication Sep. 30, 2004 Sheet 2 of 6 US 2004/0191783 A1 Row Column Symbol Gene --- 1. l hyb ctl+ Positive hyb ctl n 1 2 buffer Detection neg ctl (buffer 1 3. ARO Aromatase P450 — 4 ATM Ataxia telangiectasia mutated 1. 5 Bsg |Basigin -.... --- 6 ba BCL-2 associated athanagene 7 bak BCL2-antagonist/killer 1 1 8 bax BCL2-associated X protein - 9 bcar 1 Breast cancer anti-estrogen resistance 1 2 1 bc12 B-cell lymphoma2 2 2 bclx BCLX 2 3 Sii Sii1 2 4 bc ATP-binding cassette, sub family G member 2 2 5 23 KDa higly basic 2 6 Beclinil 2 7 ISA SiiA 2 8 breal Breast cancer 1, V 2 9 broa2 Breast cancer 2 3 1. Hyb Ctl - Negative hyb CTL 3 2 aldo aldolase A 3 3 cdhl Cadherine1/E-cadherine 3 4 cadill Cadherinell 3 5 cad 13 Cadherine 13 - 3 6 catb catenin, beta 1 3 7 ctsb cathepsinB 3 8 ctsd cathepsinD 3 9 ctsL cathepsinL 4 l cav1 Caveoline1 --- 4 2 cd44 CD44 antigen Carcinoembryonic antigen-related cell 4 CCa adhesion molecule 5 4 CmyC c-myc - - - - - - 4 cSfl colony stimulating factor 1 4 6 cSflr colony stimulating factor 1 receptor 4 7 con26 Connexine 26 4 8 Tubul alpha-Tubuline -- 9 con43 Connexine 43 5 1 cnd 1 cyclinD1 - 5 2 p16 Cyclin dependent kinase inhibitor 2A - -- 5 3 p21 Cyclin dependent kinase inhibitor 1A - 5 4 p27 Cyclin dependent kinase inhibitor 1B 5 5 ACTB Beta actine 5 6 p57 Cyclindependent kinase inhibitor l C 5 7 Sii Sii 5 8 Cystatin A Patent Application Publication Sep. 30, 2004 Sheet 3 of 6 US 2004/0191783 A1 5 9| buffer Detection neg ctl (buffer 6 cst6 Cystatin M Row I Column Symbol Gene 6 2 krt8 Cytokératine 8 6 3 ISE4 - Sh4 6 4 krt 18 Cytokératine 18 6 5 krt 19 Cytokératine 19 : 6 ecgf Endothelial cell growth factor 6 7 egfr Epidermal growth factor receptor | 6 8 Eukaryotic translation initiation factor 4E 6 9 EMS1 7 1. Estrogen receptor alpha 7 2 Estrogen receptor beta 7 3 Factor von willcbrand H.- 7 4 fibroblast growth factor 8 7 5 fibroblast growth factor 2 -- 7 6 Fibroblast growth factor receptor 7 7 fragile histidine triad gene 7 8 cyclophilin 33 A 7 9 Negative hyb CTL 8 elsoline 8 2 Glutathione S-transferase pi 8 3 hgf Hepatocyte growth factor - 4 - hgfr Hepatocyte growth factor receptor 8 5 ing Inhibitor of growth family, member 1 8 6 itga6 Integrin alpha 6 8 7 itgav Integrin alpha V 8 itgbl Integrin betal 9 itgb3 Integrine beta 3 1 ibsp Integrin-binding sialoprotein 2 illa | Interleukine 1 alpha 3 Si2 -- - Si2 illb Interleukin1 beta - GAPD Glyceraldehyde-3-phosphate-dehydrogenase il6 Interleukin 6 IS#5 ISS il8 Interleukin 8 Intcrleukin 11 Negative hyb CTL Intracellular adhesion moleculc Kangail Kallikrein 2/3 Kiss 1 metastasis supressor Mammaglobinel Maspin / Serine proteinase inhibitor clade b member 5 Patent Application Publication Sep. 30, 2004 Sheet 4 of 6 US 2004/0191783 A1 11 2 HPRT Hypoxanthine phosphoribosyltransferase Row Column Symbol Gene 1 3 mmp1 matrix metalloproteinase 1 l 4 mnp2 matrix metalloproteinase2 1 5 mmn3 matrix metalloproteinase 3 11 6 mp7 matrix metalloproteinase 7 11 7 mmp9 matrix mctalloproteinase 9 8 mmp 11 matrix metalloproteinase 11 11| 9 mmp13 matrix metalloproteinase 13 12 1. mmp 14 matrix metalloproteinase 14 12 2 mmp15 matrix metalloproteinase 15 12 3 ISS SHS 12 - 4 mdim2 MDM2 12 5 mdrl Multidrug resistant 1 mrp1 ATP-binding cassette, sub-family C 12 6 CFTR/MRP), member 1 12 7 mucl Mucine 1, transmembranaire 12 8 mucl 8 Melanoma cell adhesion molecule 2 9 nm23b Non-metastatic cells 2/1 13 1 buffer Detection neg ctl (buffer) 13 2 incoal Nuclear reptor coactivator 1 13 3 incoa2 Nuclear receptor coactivator 2 - - - 13 4 incoa3 Nuclear receptor coactivator 3 13 5 MDH Malate deshydrogenase 13 6 incorl Nuclear receptor co-repressor 1 13 7 Si2 SH2 13 8 ncor2 Nuclear receptor co-repressor 2 13 9 ASC2 Nuclear receptor co-repressor 6 14 odc Ornithine decarboxylasel 14 2 PLA2 Phospholipase A2 - - Tumor necrosis factor receptor superfamily, H 14 3 Opg member 1 lb Prolactin induced protein (gross cystic disease 14 4 gcdfp fluid protein - - 14 5 Progesterone receptor 4 6 Prostaglandin endoperoxidase synthase 2 14 7 pail plasminogen activator inhibitor typel 14 8 pai2 plasminogen activator inhibitor type2 14 9 Hyb Ct- Negative hyb CTL 15 1. phlh Parathyroid hormone-like hormone 15 2 OCa Proliferating cell nuclear antigen - 15 3 tff Trefoil factor 1 15 4 rank Receptor activator of NFkB ligand 15 5 rankl Receptor activator of NFkB |- 15 6 rb 1 Retinoblastomel 15 7 Si6 Si6. - 15 8 s100a4 S100 calcium binding protein A4 15 9 Sprl SPR1 protein 16 1 H vb Ct Patent Application Publication Sep. 30, 2004 Sheet 5 of 6 US 2004/0191783 A1 16 2 Sral |Steroid receptor RNA activator 1 Row Column Symbol Gene H- 6 3 Si3 Si3 16 4. sod2 Superoxide dismutase2 16 5 S9 Proteine S9 16 6 tipl Tight junction protein 1 16 7 Stat Stathmin 16 8 tsp Thrombospondin 1 16 9 tsp2 Thrombospondin2 17 1 tb10 Thymosin beta 10 17 2 SDS Serine deshydrogenase 17 m V 3 timp1 Tissue inhibitor of metalloproteinasel 17 4 timp2 Tissue inhibitor of metalloproteinase2 - 7 5 top2 topoisomerase2-alpha 17 6. tnfa tumor necrosis factor alpha 17 7 p53 Tumor protein p53 17 8 tpa Plasminogen activator tissue 17 - - plau Urokinase 8 uPAR Urokinase-receptor - 18 2 vegf Vascular endothelial growth factor 18 3 Si6. Si6. 18 4 vegfb Vascular endothelial growth factor B 18 5 TFR transferrin receptor 8 6 vegfc Vascular endothelial growth factor C 7 Si3 Si3 8 vegfd Vascular endothelial growth factor D 9 vegfr1 Vascular endothelial growth factor receptor1 hyb ct + Positive hyb ct 2 buffer Detection negctl (buffer) 3 Vegfr2 Vascular endothelial growth factor receptor2 4 vegfri Vascular endothelial growth factor receptor: V-erb-b2 erythroblastic leukemia viral oncogene homolog2, neuro/glioblastoma 5 erbb2 derived oncogene homolog 6 vim Vimentine 7 buffer Detection neg ctl (buffer) 8 buffer Detection negctl (buffer) - 9 buffer Detection neg ctl (buffer) 1 1 ct + Positive detection ct 2 2 ct -- Positive detection ct - 3 3ctl+ Positive detection ct 4 4 ct + Positive detection ct 5 5 ct + Positive detection ctl - 6 6 etlt Positive detection ct 7 7 et -- Positive detection ct 8 8 ct - Positive detection ct 9 9 ct + Positive detection ct 10 ct -- Positive detection ct 2 11 ct - | Positive detection ctl Patent Application Publication Sep. 30, 2004 Sheet 6 of 6 US 2004/0191783 A1 21 3 buffer Detection neg ctl (buffer Row Column Symbol Gene t 21 buffer Detection negctl (buffer buffer Detection negctl (buffer buffer Detection neg ctl (buffer) -- buffer Detection neg ctl (buffer) buffer Detection neg ctl (buffer) - - - buffer Detection neg ctl (buffer) US 2004/0191783 A1 Sep. 30, 2004 LOW DENSITY MICRO-ARRAY ANALYSIS IN 0007. In the past few decades, molecular biology tech HUMAN BREAST CANCER niques have raised Some hope to replace conventional clinico-pathological techniques. To this end a tissue Sample, BACKGROUND OF THE INVENTION Suspected to have developed cancer, is investigated prima rily on the basis of genes, in particular their expression, 0001. The present invention pertains to the field of diag which genes are known and/or Suspected to be involved in nosis and prognosis of human breast cancer. In particular, the onset and progression of cancer. the present invention pertains to a method of diagnosing the onset of breast cancer and allowing a reliable prognosis of 0008 So far a variety of different genes have been its future development.
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