Prostate cancer diagnosis and outcome prediction by expression analysis

• US 6,949,342 B2
• Filed: 12/19/2002
• Issued: 09/27/2005
• Est. Priority Date: 12/21/2001
• Status: Expired due to Fees

• Current Assignee: Dana-Farber Cancer Institute, Whitehead Institute for Biomedical Research
• Original Assignee: Dana-Farber Cancer Institute, Whitehead Institute for Biomedical Research
• Inventors: Golub, Todd R., Sellers, William R., Ross, Kenneth N., Febbo, Phillip G.
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US10/325,457
• Publication Number:
  US 20030152980A1
• Time in Patent Office: 1,013 Days
• Field of Search: 435/6, 435/7.1, 435/7.9, 435/91.1, 435/91.2, 536/23.1, 536/24.3, 536/24.33
• US Class Current: 435/6.14
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G01N 2800/52 Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Abstract

Methods identifying prostate cancer, methods for prognosing and diagnosing prostate cancer, methods for identifying a compound that modulates prostate cancer development, methods for determining the efficacy of a prostate cancer therapy, and oligonucleotide microarrays containing probes for genes involved in prostate cancer development are described.

Claims

1. A method of identifying prostate cancer comprising determining a gene expression profile from a gene expression product of at least one prostate cancer identification informative gene having increased expression in prostate cancer in a sample from prostate tissue,

wherein said at least one prostate cancer identification informative gene is HOXC6;

and wherein increased expression of said gene expression product in said sample is indicative of prostate cancer.

4. The method of any one of claims 1, or 2, or 3, comprising further determining a gene expression profile from a gene expression product of at least one additional prostate cancer identification informative gene having increased expression in prostate cancer, wherein said prostate cancer identification informative gene is selected from the group consisting of:

the genes identified by UniGene Cluster Nos. Hs.154424, Hs.823, Hs.79037, Hs.112259, Hs.82280, Hs.4815, Hs.149923, Hs.164280, M21535, Hs.75655, X17620, Hs.574, Hs.182426, Hs.7780, Hs.90336, Hs.25640, Hs.149923, Hs.38972, Hs.83190, Hs.164280, Hs.163593, Hs.73742, Hs.753109, Hs.28491, Hs.182527, Hs.79217, Hs.79093, Hs.10247, Hs.56145, Hs.182979, Hs.2795, Hs.76230, Hs.119122, Hs.181634, Hs.10082, Hs.183698, Hs.75432, Hs.76136, Hs.180842, Hs.227823, Hs.158675, Hs.69469, Hs.75362, Hs.91011, Hs.111029, Hs.155560, Hs.180911, Hs.21543, Hs.1832, Hs.118690, Hs.75212, Hs.22751 1, Hs.155048, Hs.106778, Hs.65114, Hs. 174131, Hs.178551, Hs.153177, Hs.146763, Hs.75538, Hs.133230, Hs.105440, Hs.186570, Hs.184270, Hs.83383, Hs.8752, Hs.146763, Hs.76422, Hs.135, Hs.76698, Hs.I 117950, Hs.74267, Hs.89529, Hs.5662, Hs.83753, Hs.2953, Hs.1708, Hs179516, Hs.110029, Hs.76285, Hs.4112, Hs.3491, Hs.56845, Hs.5174, Hs.1197, Hs.6727, Hs.75525, Hs.161002, Hs.75471, Hs.1066, Hs.75139, Hs.76194, Hs.180450, Hs.75207, Hs.61273, Hs.51299, Hs.111611, Hs.234489, Hs.6456, Hs.178391, Hs.16492, Hs.75458, Hs.75459, Hs.82202, Hs.25846, Hs.70337, Hs.180946, Hs.198951, Hs.74861, Hs.179779, Hs.4193, Hs.184776, Hs.158675, Hs.174140, Hs.61635, Hs.126701, Hs.75789, Hs.848, Hs.6895, Hs.8603, Hs.5809, Hs.170250, Hs.31130, Hs.172089, Hs.286, Hs.699, Hs.179943, Hs.165590, Hs.75724, Hs.180414, Hs.75746, Hs.75616, Hs.234518, Hs.80617, Hs.182825, Hs.184582, Hs.181350, Hs.76067, Hs.13456, Hs.70830, Hs.155356, Hs.163867, Hs.130227, Hs.84072, Hs.3297, Hs.5662, Hs.119252, Hs.10842, Hs.79081, Hs.49346, Hs.18953, Hs.1948, Hs.136644, Hs.7306, Hs.4437, Hs.182740, Hs.76064, Hs.6574, Hs.118065, Hs.211824, Hs.154890, Hs.154103, Hs. 106711, Hs. 129548, Hs.180737, Hs.79, Hs.74276, Hs.185057, Hs.169301, Hs.31439, Hs.118638, Hs.172182, Hs.75914, Hs.9950, Hs.82148, Hs.78614, Hs.203907, Hs.73818, Hs.82148, Hs.2953, Hs.166033, Hs.119076, Hs.5174, Hs.66762, Hs.181243, Hs.06673, Hs.55682, Hs.9701, Hs.183109, Hs.75344, Hs.119387, Hs.113029, Hs.119598, Hs.75722, Hs.93304, Hs.120856, Hs.184014, Hs.169793, Hs.234705, Hs.75618, Hs.5957, Hs.63552, Hs.74405, Hs.75744, Hs.118836, Hs.105465, Hs.177559, Hs.7771, Hs.173205, Hs.157850, Hs.101025, Hs.70830, Hs.3128, Hs.28757, Hs.77290, Hs.32317, Hs.9235, Hs.12770, Hs.114360, Hs.15071, Hs.184582, Hs.8123, Hs.83753, Hs.17144, Hs.3709, Hs.145279, Hs.30965, Hs.182429, Hs.89674, Hs.91747, Hs.74624, Hs.84359, Hs.74407, Hs.28914, Hs.182371, Hs.7314, Hs.77257, Hs.182937, Hs.75607, Hs.238542, Hs.93659, Hs.84131, Hs.76847, Hs.49767, Hs.98732. Hs.15832, HS.75410, Hs.180352, Hs. 41569, Hs.2642, Hs.75893, Hs.121017, Hs.878, Hs.109201, Hs.109752, Hs.7936, Hs.3462, Hs.199263, Hs.94466, Hs.83532, Hs.230, Hs.166152, Hs.11223, Hs.4890, Hs.91379, Hs.1624, Hs.6396, Hs.234518, Hs.89643, Hs.51860, Hs.S5971, Hs.S52721, Hs.S5591, Hs.S1908, Hs.S3389, Hs.S2453, Hs.S3950, Hs.S81622 1, Hs.S6082, Hs.S5945, Hs.S569401, Hs.S417477, Hs.54651, Hs.S572086, Hs.S268597, Hs.S1369068, Hs.70823, Hs.77290, Hs.82226, Hs.118162, Hs.80988, Hs.129872, Hs.179573, Hs.178551, Hs.178728, Hs.142827, Hs.271473, Hs.77054, Hs.7969 1, Hs.154424, Hs.75860, Hs.82932, Hs.82163, Hs.125078, Hs.85181, Hs.26077, Hs.1255, Hs.79, Hs.80768, Hs.89781, Hs.75916, Hs.194673, Hs.74368, Hs.83920, Hs.18593, Hs.146550, Hs.198281, Hs.814, Hs.10247, Hs.75074, Hs.2064, Hs.279554, Hs.76884, Hs.119529, Hs.182366, Hs.179573, Hs.25348, Hs.90786, Hs.I 18397, Hs.77326, Hs.108660, Hs.108623, Hs.203917, Hs.7278, Hs.118223, Hs.17409, Hs.111779, Hs.11494, Hs.821, Hs.178658, Hs.288869, Hs.75248, Hs.288031, Hs.108623, Hs.1650, Hs.287820, Hs.111779, Hs.178551, Hs.182825, Hs.7252, Hs.75447, Hs.31130, Hs.172182, Hs.306965, Hs.83920, Hs.83920, Hs.76144, Hs.76144, Hs.142827, Hs.302649, Hs.302649, Hs.347991, Hs.29131, Hs.8546, Hs.75283, Hs.6909, Hs.82045, Hs.82045, Hs.83337, Hs.70823, Hs.119206, Hs.119206, Hs.77326, Hs.76884, Hs.268371, Hs.820, Hs.82226, Hs.334695, Hs.287820, Hs.58189, Hs.2642, Hs.243901, Hs.18593, Hs.111680, Hs.76753, Hs.184693, Hs.9295, Hs.9295, Hs.351875, Hs.70327, Hs.17409, Hs.344027, Hs.179573, Hs.179573, Hs.179573, Hs.81800, Hs.81800, Hs.1584, Hs.1584, Hs.77054, Hs.108660, Hs.108660, Hs.169401, Hs.268571, Hs.118397, Hs.72157, Hs.111222;

the genes identified by GenBank Accession Nos. D14530, X58965, U37518, J04152, M55409, M14199, M99487, U 51004, Z97630, J02783, X63527, U21090, M22430, L19686, U41060, M64241, M1 1353, X56468, U95006, U18321, D38047, AL035252, M21154, D13748, M55914, M34309, U70063, D38048, AB000584, X73066, AL021546, U76604, X15187, AL034374, M84711, X00734, M33764, M21154, M99487;

M93036;

the genes identified by hybridization to probe 1513_at, 1173_g at, 179_at, 1180_g_at, 296_at, 1840_g_at or 324_f_at in the Affymetrix®

Human Genome U95Av2 Array;

platelet derived growth factor receptor beta, and chromogranin A.

6. The method of claim 1, 2, 3, 4, or 5, wherein said method comprises determining the gene expression profile from the gene expression product of at least four prostate cancer identification informative genes.

7. The method of claim 1, 2, 3, 4, or 5, wherein said method comprises determining the gene expression profile from the gene expression product of at least sixteen prostate cancer identification informative genes.

2. A method of predicting the likelihood of prostate cancer development in a subject, comprising determining a gene expression profile from a gene expression product of at least one informative gene having increased expression in prostate cancer in a sample, derived from prostate tissue;

wherein said at least one prostate cancer identification informative gene is HQXC6;

and wherein increased expression of said gene in said sample indicates an increased likelihood of prostate cancer development in the subject.

5. The method of claim 2, 3, or 4, comprising further determining a gene expression profile from a gene expression product of at least one prostate cancer identification informative gene having decreased expression in prostate cancer, wherein said at least one prostate cancer identification informative gene is selected from the group consisting of:

the genes identified by UniGene Cluster Nos. Hs.155597, Hs.8272, Hs.79389, Hs.236327, Hs.101850, Hs.7974, Hs.8022, Hs.81256, Hs.80395, Hs.85087, Hs.106070, Hs.173594, Hs.2463, Hs.18586, Hs.1940, Hs.166072, Hs.211819, Hs.56045, Hs.30250, Hs.9552, Hs.117782, M98539, Hs.6349, Hs.9999, Hs.76688, Hs.173381, Hs.78065, Hs.156007, Hs.95420, Hs.80206, Hs.220056, Hs.75350, Hs.9651, Hs.75586, Hs.8025, Hs.6606, Hs.75106, Hs.85155, Hs.104105, Hs.66392, Hs.82794, Hs.29736, Hs.77546, Hs.171595, Hs.226795, Hs.112844, Hs.7833, Hs.160483, Hs.227716, Hs.93557, Hs.74034, Hs.106826, Hs.82001, Hs.19180, Hs.20060, Hs.3407, Hs.81047, Hs.25511, Hs.9208, Hs.8402, Hs.137569, Hs.37682, Hs.154721, Hs.46659, Hs.1640, Hs.35094, Hs.76536, Hs.231884, Hs.65424, Hs.78989, Hs.184724, Hs.198689, Hs.109438, Hs.79386, Hs.48998, Hs.126084, Hs.29802, Hs.80552, Hs.35861, Hs.170133, Hs.74070, Hs.14896, Hs.84883, Hs.82749, Hs.82109, Hs.10351, Hs.114346, Hs.160318, Hs.20084, Hs.12956, Hs.21851, Hs.75807, Hs.4217, Hs.202097, Hs.239587, Hs.7835, Hs.77448, Hs.76884, Hs.20144, Hs.118796, Hs.234680, Hs.13999, Hs.79844, Hs.75899, Hs.170279, Hs.188882, Hs.21858, Hs.78629, Hs.134932, Hs.107164, Hs.82223, Hs.19368, Hs.50130, Hs.105584, Hs.78501, Hs.6139, Hs.225936, Hs.195432, Hs.155122, Hs.35094, Hs.167740, Hs.8762, Hs.155119, Hs.47431, Hs.8309, Hs.1473, Hs.158348, Hs.845, Hs.200188, Hs.123659, Hs.161166, Hs.180533, Hs.79844, Hs.214142, Hs.82128, Hs.79101, Hs.170917, Hs.76873, Hs.99877, Hs.36975, Hs.234759, Hs.12256, Hs.194143, Hs.94581, Hs.46329, Hs.77578, Hs.181202, Hs.76719, Hs.258850, Hs.195484, Hs.75180, Hs.2025, Hs.110746, Hs.211562, Hs.2726, Hs.5457, Hs.121478, Hs.250773, Hs.9059, Hs.21894, Hs.124029, Hs.169401, Hs.80261, Hs.122575, Hs.126256, Hs.51, Hs.278540, Hs.79432, Hs.203, Hs.37501, Hs.194657, Hs.7678, Hs.49378, Hs.158297, Hs.95243, Hs.1372, Hs.27973, Hs.12513, Hs.84, Hs.272951, Hs.123125, Hs.66542, Hs.166361, Hs.156115, Hs.199179, Hs.24103, Hs.2664, Hs.173894, Hs.23294, Hs.274295, Hs.4764, Hs.155987, Hs.35861, Hs.69171, Hs.80343, Hs.78765, Hs.69351, Hs.66774, Hs.99877, Hs.89499, Hs.96744, Hs.184194, Hs.23964, Hs.2994, Hs.6441, Hs.89633, Hs.635, Hs.1074, Hs.143522, Hs.137570, Hs.227473, Hs.23777, Hs.172670, Hs.158029, Hs.166074, Hs.26837, Hs.29287, Hs.250615, Hs.172690, Hs.180034, Hs.154846, Hs.239459, Hs.158112, Hs.180224, Hs.4278, Hs.4105, Hs.25333, Hs.79353, Hs.79241, Hs.90419, Hs.19261, Hs.155140, Hs.50964, Hs.40300, Hs.123090, Hs.103915, Hs.95197, Hs.2316, Hs.239926, Hs.248059, Hs.44131, Hs.54413, Hs.13531, Hs.105924, Hs.250616, Hs.340, Hs.77889, Hs.92614, Hs.236774, Hs.2860, Hs.75438, Hs.172674, Hs.1378, Hs.183037, Hs.179574, Hs.5105, Hs.183752, Hs.158164, Hs.169849, Hs.4055, Hs.31074, Hs.274416, Hs.514, Hs.166096, Hs.78993, Hs.154762, Hs.2253, Hs.55879, Hs.166051, Hs.78880, Hs.74624, Hs.80247, Hs.771 83, Hs.77183, Hs.23582, Hs.14894, Hs.2025, Hs.158287, Hs.2316, Hs.2554, Hs.138860, Hs.26550, Hs.35861, Hs.74624, Hs.152978, Hs.96744, Hs.2860, Hs.117780, Hs.93841, Hs.31074, Hs.5025, Hs.78344, Hs.183752, Hs.183752, Hs.283655, Hs.93199, Hs.177664, Hs.103915, Hs.89868, Hs.171995, Hs.171995, Hs.190913, Hs.250616, Hs.82112, Hs.78877, Hs.22111, Hs.3268, Hs.115352, Hs.155546, Hs.306122, Hs.343871, Hs.336920, Hs.2704, Hs.77889, Hs.183738, Hs.159543, Hs.166096, Hs.103854, Hs.2253, Hs.173894, Hs.164410, Hs.80247, Hs.76722, Hs.12, Hs.50964, Hs.287921, Hs.75462, Hs.193163, Hs.193163, Hs.31210, Hs.176658, Hs.75741, Hs.95197, Hs.154721, Hs.1852, Hs.194750, Hs.419, Hs.158029, Hs.323053, Hs.323053, Hs.323053, Hs.323053, Hs.128425, Hs.166079, Hs.166079, Hs.301373, Hs.117729, Hs.289106, Hs.169848, Hs.239, Hs.2780, Hs.336920;

the genes identified by GenBank Accession Nos. D00017, M96233, X14885, L07594, U04313, X57025, L13720, X02958, L24203, U21689, U93305, M14752, L37112;

the genes identified by hybridization to probe 1664_at or 40735_at in the Affymetrix®

Human Genome U95Av2 Array;

inositol triphosphate receptor type 3 and beta galactoside sialotransferase;

wherein increased expression of HOXC6 and decreased expression of at least one of the prostate cancer identification informative genes identified in this claim is indicative of prostate cancer.

3. A method of diagnosing prostate cancer in a subject, comprising determining a gene expression profile from a gene expression product of at least one informative gene having increased expression in prostate cancer in a sample from prostate tissue;

wherein said at least one prostate cancer identification informative gene is HOXC6;

and wherein increased expression of said gene in said sample indicates the presence of prostate cancer in said subject.