Abnormal hedgehog signaling, most commonly caused by loss of PTCH1 inhibitor activity,drives tumorigenesis of basal cell carcinomas (BCCs). To assess whether other tumors also have abnormal hedgehog signaling, we have assayed RNA from common cancers at nine different sites for levels of expression of hedgehog target genes that are up-regulated uniformly in BCCs. We report here that such dysregulation appears not to be common in the types of non-BCC cancers studied, indicating that the molecular pathogenesis of BCCs, like their frequency and behavior, differs markedly from that of most other cancers.

Abnormalities of hedgehog signaling have been identified as the master switch controlling the abnormal behavior of BCCs,3 the commonest human cancer (1, 2). These abnormalities can arise by somatic mutations in genes encoding several of the molecules that mediate hedgehog signaling; heritable mutations in PTCH1, an inhibitor of hedgehog signaling, underlie the BCNS. The latter is a hereditary syndrome in which patients are at increased risk not only for BCCs but also for medulloblastomas, rhabdomyosarcomas, odontogenic and epidermal cysts, and perhaps for meningiomas (3). Mutations of PTCH1 and other hedgehog pathway genes occur frequently in sporadic tumors of the types that are of higher than normal incidence in BCNS patients. These include BCCs (and the related tumor trichoepitheliomas), medulloblastomas (4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18), and odontogenic cysts (19).

By contrast, limited information is available regarding hedgehog signaling in other tumors (20). Most of the available data have come from studies of two types. First, low-frequency amplifications of the region of chromosome 12q that contains GLI1 have been found in several tumor types [e.g., childhood nonrhabdomyosarcoma sarcomas (21, 22), gliomas (23, 24, 25), and B-cell lymphomas (26, 27)]. The GLI1 gene encodes a transcription factor that mediates at least some of hedgehog target gene expression, and GLI1 expression is itself up-regulated in cells responding to hedgehog ligand. However, the amplicons typically include additional genes, such as CDK4, and amplification of these other genes, but not of GLI1, occurs in some tumors. This suggests that what is critical to the growth of tumor cells carrying the 12q amplification is overexpression of one or more of these other genes rather than overexpression of GLI1 (25). Low-level up-regulation of GLI1 mRNA expression has been found in adult sarcomas without accompanying GLI1 gene amplification, and the amount of GLI1 mRNA in these tumors correlates with the degree of clinical malignancy (28). However, the genesis of this up-regulation and its contribution to the activation of expression of other target genes, let alone to the behavior of the cells, are unknown.

Second, PTCH1 mutations have been identified, albeit at low frequency, in DNA from sporadic tumors or cell lines derived from various cancers: (a) breast; (b) colon; (c) esophagus; (d) bladder; and (e) brain (10, 29, 30, 31, 32). Because PTCH1 mutations cannot be detected in DNA of many BCNS patients (33), despite uniform linkage to the site of the PTCH1 gene on chromosome 9q, or in sporadic BCCs, despite uniform dysregulation of hedgehog signaling in these tumors, it is likely that current screening detects only a fraction of PTCH1 gene mutations. Furthermore, mutations in genes encoding other participants in hedgehog signaling also may drive aberrant signaling and tumorigenesis (31, 34, 35). Therefore, currently, it is impractical to survey extracutaneous tumors adequately for pathogenetic abnormalities of this pathway simply by screening for mutations in genes encoding pathway members. Further complicating our efforts to understand the pathogenetic significance of identified mutations is the recent finding that even medulloblastomas (36), tumors in which evidence for hedgehog signaling abnormalities is excellent, may lose only one copy of the PTCH1 gene but retain apparently normal function of the other allele (37, 38).

Given the importance of more broadly assessing hedgehog signaling in cancers and the above-described technical difficulties of mutation detection, we have investigated a selection of more common sporadic extracutaneous tumors for hedgehog signaling dysregulation not indirectly by searching for mutations or amplifications but rather directly by assaying for abnormal accumulation of species of mRNA known to be induced by hedgehog signaling and uniformly up-regulated in BCCs: (a) PTCH1; (b) GLI1; (c) HIP; and (d) PDGFRα (4, 39, 40, 41, 42, 43, 44, 45, 46). We have found essentially no enhanced accumulation of any of these mRNA species in the 68 tumor specimens studied, indicating that hedgehog signaling dysregulation is not crucial to the development of most common non-BCC cancers.

Tumors and RNA Extraction.

Tumors and adjacent nontumorous tissues (both primary tumors and metastases), in excess of that needed for pathological evaluation, were collected fresh and stored initially on dry ice and then at −70°. For RNA isolation from tissues other than brain, tissues were homogenized on ice with a Polytron in guanidine isothiocyanate buffer, the homogenate was applied to a RNeasy spin column (RNeasy Midi kit; Qiagen), the column was washed, and the RNA was eluted in RNase-free water. For glioblastoma multiforme and gliotic tissues, RNA was extracted with TRIzol (Life Technologies, Inc.) and further purified to mRNA with a Fast Track oligo dT column (Invitrogen).

TaqMan mRNA Quantitation.

mRNA was quantitated using TaqMan real-time PCR amplification (PE Biosystems). All results were normalized to the amount of GAPDH mRNA in each sample. Primers and probes used were as follows: PTCH 1, Probe: 6FAM-AATTCCCGCTCTGCGGGCG-TAMRA, Primers: Forward: 5′-TCTTCATGGCCGCGTTAATC, Reverse: 5′-TTGCAGGAAAAATGAGCAGAAC; GLI1, Probe: 6FAM-TGCTGGTGGTTCACATGCGCAGA-TAMRA, Primers: Forward: 5′-TGAGGCCCTTCAAAGCCC, Reverse: 5′-ATGACTTCCGGCACCTTTC; HIP, Probe: 6FAM-TGTATGTGTCCTATACCACCAACCAAGAACGGTAMRA, Primers: Forward: 5′-TGCTAAGCCTCGCATTCCA, Reverse: 5′-ACAACCCTAAGAATGTGGTCATGA; PDGFRα, Probe: 6FAM-CCTCCAGCGAATTTCATACCTCGGTTTCT-TAMRA, Primers: Forward: 5′-CTCACTTATTGTCCTGGTTGTCATTT, Reverse: 5′-CTGCATCGGGTCCACAT; GAPDH, Probe: 6FAM-CAAGCTTCCCGTTCTCAGCC-TAMRA, Primers: Forward: 5′-GAAGGTGAAGGTCGGAGTC, Reverse: 5′-GAAGATGGTGATGGGATTTC.

Amplification was performed using 50°C for 2 min, 95°C for 10 min, followed by 40 cycles of 95°C for 15 s and 60°C for 1 min. mRNA quantitation was assessed by the fluorescence intensity emitted after PCR amplification. The difference in the fluorescence (threshold) between tubes with GAPDH amplification and those with the specific mRNA amplification was compared for tumor and normal tissue extracts.

We examined the following tumors and corresponding normal tissues: (a) bladder–2 and 1; (b) brain–16 and 2 (the latter were histologically normal samples from tissue taken from patients with epilepsy); (c) breast–15 and 6; (d) colorectal-15 and 16; (e) esophagus–2 and 2; (f) kidney–4 and 5; (g) lung–7 and 7; (h) ovary-2 and 0; (i) stomach–3 and 2; and (j) uterus–2 and 1. Matched normal tissue was obtained from all patients from whom the tumors were collected, and for most patients, both normal and tumor tissue results could be compared. The results from the normal samples at each site were quite consistent, and so we simply compared each tumor versus all available normal tissues at that site (Table 1).

In all 68 tumors examined, the mRNA encoding genes that are targets of hedgehog signaling and up-regulated uniformly in BCCs (PTCH1, GLI1, HIP, and PDGFRα) was no greater and in most instances was less than that in adjacent normal tissue.

We analyzed 15 glioblastoma multiforme tumors, one grade 3 anaplastic astrocytoma, five glioma cell lines, and one medulloblastoma cell line and found no up-regulation of hedgehog target genes. An exception to this general lack of up-regulation of hedgehog target genes in brain cancers was our finding that 6 of the 15 glioblastomas had 2–16-fold increases in PDGFRα. However, 5 of these 6 tumors had no increase in other hedgehog target genes, suggesting that the up-regulation of PDGFRα expression was driven by non-hedgehog mechanisms. The 6th brain tumor had an 8-fold increase in PTCH1 mRNA in addition to its 8-fold increase in PDGFRα mRNA but had no increase in mRNA encoding GLI1 or HIP. There were insufficient amounts of RNA available for further study of this tumor, and there were no distinguishing histological or other features of this tumor as compared with the other 14 glioblastomas.

We found no increased expression of four genes uniformly up-regulated in BCCs in extracutaneous cancers, suggesting that activation of hedgehog signaling is unlikely to be of major importance in the more common non-BCC cancers. This conclusion must be considered tentative for several reasons.

First, we have no proof that these genes actually are targets of hedgehog signaling in these tumor types. Nonetheless, PTCH1 expression is a conserved target of hedgehog signaling in organisms as diverse as humans and flies and tissues as diverse as wings, eyes, skin, and lung (47, 48, 49), making it likely that PTCH1 and/or at least one of these other well-described targets of hedgehog signaling in other cells would be a target of dysregulated hedgehog signaling in human non-BCC tumors as well. By contrast, human sporadic medulloblastomas, which occur in higher than normal incidence in BCNS patients, frequently do have PTCH1 or SMO mutations and increased PTCH1 mRNA (7, 8, 9, 10, 16, 31, 36), and at least in ptc1 +/− mice, these tumors have enhanced ptc1 promoter activity (50). Furthermore, rhabdomyosarcomas in ptc1 +/− mice have increased gli1 mRNA (51), as well as increased ptc1 promoter activity (50).

Second, there is at least one situation in which hedgehog mutations appear to influence cell behavior without causing abnormal expression of these four genes. This is the ASZ001 cell line, which was established from a mouse BCC that (like all other BCCs in ptc1 +/− mice) had elevated ptc1 promoter activity, in this instance attributable to lost functioning of both ptc1 alleles (50). This cell line also has mutations in both p53 alleles. These cells continue to proliferate at calcium concentrations sufficient to cause normal mouse epidermal keratinocytes grown from wild-type or p53-null mice to cease proliferation and undergo irreversible differentiation. Nonetheless, these cells in vitro have levels of mRNA encoding gli1, hip, and PDGFRα no higher than those of cultured normal mouse epidermal keratinocytes. Thus, it is possible that mutant ptc1 may influence cell behavior without up-regulating expression of (at least these) hedgehog target genes. The recent reports that: (a) the hedgehog pathway component smoothened is able to signal as a G protein-coupled receptor (52) and (b) PTCH1 loss may affect the cell cycle directly by releasing otherwise sequestered cyclin B (53) may be relevant to this finding.

Finally, we did not study an unlimited number of tumors, even of breast and colon/rectum, and also did not study some visceral tumors (e.g., prostate cancers and nonglioblastoma brain tumors). Hence, these, as well as less common cancers of other viscera and/or specific subtypes, may have hedgehog target gene transcriptional changes. Indeed, not only adult sarcomas (28) but also occasional nonmedulloblastoma brain cancers (54) have been reported by others to have some elevation of GLI1 message. Recently, Dahmane et al.(55) have reported the expression of GLI1 and PTCH1 in human brain cancers, not only in primitive neuroectodermal tumors but also in glial tumors. Our results are not inconsistent with theirs; we too found expression of all four tested genes in gliomas. However, we did not find expression levels to be elevated consistently; quite unlike the average 100-fold increase of expression levels in BCCs (45), and the reverse transcription-PCR results they illustrate suggest that they found considerably lower expression levels of GLI1 and PTCH1 in gliomas than in primitive neuroectodermal tumors.

Of note, nonpregnant female ptc1 +/− mice have uniformly abnormal breast ductal epithelium, resembling ductal carcinoma in situ(56). Nonetheless, none of the ductal human breast cancers that we studied had evidence of hedgehog target gene dysregulation.

It is unclear why dysregulation of this pathway appears to be limited to those tumors also found in increased incidence in BCNS patients because that is not the case for other tumor suppressor genes whose mutations underlie hereditary human cancer syndromes (e.g., p53/Li-Fraumeni syndrome). This discrepancy should be considered against the background of the extremely high incidence of BCCs, an incidence that is as high in some Caucasian populations as is their incidence of all other cancers combined. At least three possible explanations seem formally possible: (a) genes encoding proteins active in the hedgehog signaling pathway may be especially susceptible to UV radiation mutagenesis; against this possibility is the finding that BCCs induced in ptc1 +/− mice by ionizing radiation also have hedgehog dysregulation (50) as do BCCs arising on sun-protected parts of the body, such as the back and chest; (b) other cells may possess redundant hedgehog-restraining mechanisms lacking in keratinocytes, and hence they may achieve hedgehog dysregulation less easily; and (c) the behavior of adult cells other than keratinocytes may be less sensitive to the effects of hedgehog dysregulation. Studies of forced up-regulation of hedgehog target genes in extracutaneous tissues should help differentiate between these latter two possibilities.

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

1

Supported by NIH Grants CA 81888-01 (to E. H. E.) and CA44968 (Cooperative Human Tissue Network), as well as generous gifts from the Michael Rainen Family Foundation and Patricia Hughes. Tissue samples were provided by the Cooperative Human Tissue Network, which is funded by the National Cancer Institute (CA44968), and the University of California at San Francisco Brain Tumor Research Institute. Other investigators may have received specimens from the same subjects.

3

The abbreviations used are: BCC, basal cell carcinoma; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; BCNS, basal cell nevus syndrome.

Table 1

Tumor characteristics and Hedgehog target gene expression in cancersa

Bladder
NormalSample no.SexRacebAgeHistologyPtcGliPDGFRαHip
 479 83 Normal tissue  5.9 2.8 0.2 1.5 
Tumor Sample no. Sex Race Age Histology  Ptc Gli PDGFRα Hip 
 480 83 Transitional cell carcinoma, invasive, poorly differentiated  10.3 6.6 3.6 8.1 
 460 88 Transitional cell carcinoma, invasive, poorly differentiated  7.6 6.2 5.4 7.3 
      Average 9.0 6.4 4.5 7.7 
Bladder
NormalSample no.SexRacebAgeHistologyPtcGliPDGFRαHip
 479 83 Normal tissue  5.9 2.8 0.2 1.5 
Tumor Sample no. Sex Race Age Histology  Ptc Gli PDGFRα Hip 
 480 83 Transitional cell carcinoma, invasive, poorly differentiated  10.3 6.6 3.6 8.1 
 460 88 Transitional cell carcinoma, invasive, poorly differentiated  7.6 6.2 5.4 7.3 
      Average 9.0 6.4 4.5 7.7 
Brain
NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 33 Gliosis  7.6 7.4 5.2 4.8 
 12 Gliosis  7.5 4.8 4.8 6.8 
      Average 7.6 6.1 5.0 5.8 
Brain
NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 33 Gliosis  7.6 7.4 5.2 4.8 
 12 Gliosis  7.5 4.8 4.8 6.8 
      Average 7.6 6.1 5.0 5.8 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 28 AAIII  6.7 10.8 2.4 6.1 
 38 Glioblastoma multiforme  4.6 6.9 2.0 5.8 
 67 Glioblastoma multiforme  7.4 8.8 7.4 8.9 
 78 Glioblastoma multiforme  8.5 9.2 8.6 8.7 
 73 Glioblastoma multiforme  8.5 9.9 6.3 8.6 
 44 Glioblastoma multiforme  10.6 14.1 1.6 8.1 
 70 Glioblastoma multiforme  7.1 7.9 3.2 9.0 
 10 58 Glioblastoma multiforme  7.6 9.4 3.6 9.3 
 11 68 Glioblastoma multiforme  8.7 10.4 5.4 6.5 
 12 Glioblastoma multiforme  7.5 10.9 7.1 6.0 
 13 74 Glioblastoma multiforme  8.8 8.8 4.4 8.3 
 14 69 Glioblastoma multiforme  9.2 9.7 4.6 8.5 
 15 71 Glioblastoma multiforme  6.2 9.2 3.9 6.2 
 16 61 Glioblastoma multiforme  6.4 6.1 7.1 7.1 
 17 13 Glioblastoma multiforme  6.3 9.4 0.2 8.2 
 18 35 Glioblastoma multiforme  6.9 9.5 3.1 7.6 
      Average 7.6 9.4 4.4 7.7 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 28 AAIII  6.7 10.8 2.4 6.1 
 38 Glioblastoma multiforme  4.6 6.9 2.0 5.8 
 67 Glioblastoma multiforme  7.4 8.8 7.4 8.9 
 78 Glioblastoma multiforme  8.5 9.2 8.6 8.7 
 73 Glioblastoma multiforme  8.5 9.9 6.3 8.6 
 44 Glioblastoma multiforme  10.6 14.1 1.6 8.1 
 70 Glioblastoma multiforme  7.1 7.9 3.2 9.0 
 10 58 Glioblastoma multiforme  7.6 9.4 3.6 9.3 
 11 68 Glioblastoma multiforme  8.7 10.4 5.4 6.5 
 12 Glioblastoma multiforme  7.5 10.9 7.1 6.0 
 13 74 Glioblastoma multiforme  8.8 8.8 4.4 8.3 
 14 69 Glioblastoma multiforme  9.2 9.7 4.6 8.5 
 15 71 Glioblastoma multiforme  6.2 9.2 3.9 6.2 
 16 61 Glioblastoma multiforme  6.4 6.1 7.1 7.1 
 17 13 Glioblastoma multiforme  6.3 9.4 0.2 8.2 
 18 35 Glioblastoma multiforme  6.9 9.5 3.1 7.6 
      Average 7.6 9.4 4.4 7.7 
Tumor cell linesSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 Daoy Medulloblastoma cell line  7.3 7.8 9.3 7.4 
 SF767 50 Glioma cell line  10.5 8.3 15.8 16.9 
 U251 75 Glioma cell line  10.5 7.4 5.1 13.5 
 LN229 60 Glioma cell line  7.2 9.0 9.1 10.6 
 SNB19 Glioma cell line  10.1 12.5 3.2 10.7 
 U87 44 Glioma cell line  11.4 8.7 10.6 16.1 
      Average 9.5 9.0 8.9 12.9 
Tumor cell linesSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 Daoy Medulloblastoma cell line  7.3 7.8 9.3 7.4 
 SF767 50 Glioma cell line  10.5 8.3 15.8 16.9 
 U251 75 Glioma cell line  10.5 7.4 5.1 13.5 
 LN229 60 Glioma cell line  7.2 9.0 9.1 10.6 
 SNB19 Glioma cell line  10.1 12.5 3.2 10.7 
 U87 44 Glioma cell line  11.4 8.7 10.6 16.1 
      Average 9.5 9.0 8.9 12.9 
Breast NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 330 36 Normal tissue  5.4 3.4 2.1 4.7 
 332 50 Normal tissue  6.7 5.6 2.2 9.4 
 333 52 Normal tissue  5.3 3.7 1.6 6.5 
 407 68 Normal tissue  6.4 4.8 4.8 8.9 
 429 54 Normal tissue  5.3 6.0 3.9 7.8 
 508 49 Normal tissue  6.6 5.3   
      Average 6.0 4.8 2.9 7.5 
Breast NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 330 36 Normal tissue  5.4 3.4 2.1 4.7 
 332 50 Normal tissue  6.7 5.6 2.2 9.4 
 333 52 Normal tissue  5.3 3.7 1.6 6.5 
 407 68 Normal tissue  6.4 4.8 4.8 8.9 
 429 54 Normal tissue  5.3 6.0 3.9 7.8 
 508 49 Normal tissue  6.6 5.3   
      Average 6.0 4.8 2.9 7.5 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 323 51 Ductal carcinoma, infiltrating, moderately differentiated  8.8 11.4 7.2 10.1 
 324 50 Ductal carcinoma, in situ and invasive  5.5 4.8 5.7 6.7 
 331 36 Ductal carcinoma, invasive  9.1 11.1 6.7 12.8 
 334 52 Ductal and lobular carcinoma  10.7 9.2 5.7 11.1 
 401 67 Adenocarcinoma, mucinous type  12.0 11.9 7.1 11.2 
 403 44 Ductal carcinoma, invasive  6.4 4.3 4.8 7.2 
 408 40 Medullary carcinoma  5.9 8.7 6.6 10.1 
 430 54 Ductal carcinoma, invasive  7.0 7.7 4.7 9.5 
 434 6.1 Ductal carcinoma, invasive  11.9 12.2 5.8 9.4 
 436 69 Ductal carcinoma, infiltrating invasive, moderately differentiated  7.6 4.3 3.0 7.0 
 449 53 Ductal carcinoma, infiltrating invasive, poorly differentiated  11.8 10.9 8.8 11.8 
 465 62 Cystosarcoma phyllodes, malignant  8.5 6.3 3.3 8.3 
 472 42 Ductal carcinoma, invasive  10.4 10.2 3.4 11.6 
 501 36 Ductal carcinoma, invasive  10.8 7.1 3.8 9.6 
 509 49 Ductal carcinoma, invasive  10.5 9.3 5.2 11.6 
      Average 9.1 8.6 5.5 9.9 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 323 51 Ductal carcinoma, infiltrating, moderately differentiated  8.8 11.4 7.2 10.1 
 324 50 Ductal carcinoma, in situ and invasive  5.5 4.8 5.7 6.7 
 331 36 Ductal carcinoma, invasive  9.1 11.1 6.7 12.8 
 334 52 Ductal and lobular carcinoma  10.7 9.2 5.7 11.1 
 401 67 Adenocarcinoma, mucinous type  12.0 11.9 7.1 11.2 
 403 44 Ductal carcinoma, invasive  6.4 4.3 4.8 7.2 
 408 40 Medullary carcinoma  5.9 8.7 6.6 10.1 
 430 54 Ductal carcinoma, invasive  7.0 7.7 4.7 9.5 
 434 6.1 Ductal carcinoma, invasive  11.9 12.2 5.8 9.4 
 436 69 Ductal carcinoma, infiltrating invasive, moderately differentiated  7.6 4.3 3.0 7.0 
 449 53 Ductal carcinoma, infiltrating invasive, poorly differentiated  11.8 10.9 8.8 11.8 
 465 62 Cystosarcoma phyllodes, malignant  8.5 6.3 3.3 8.3 
 472 42 Ductal carcinoma, invasive  10.4 10.2 3.4 11.6 
 501 36 Ductal carcinoma, invasive  10.8 7.1 3.8 9.6 
 509 49 Ductal carcinoma, invasive  10.5 9.3 5.2 11.6 
      Average 9.1 8.6 5.5 9.9 
Colorectal
Normal tissueSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 321 85 Normal tissue  6.0 6.4 4.5 6.2 
 328 73 Normal tissue  6.3 5.2 3.3 7.5 
 417 61 Normal tissue  4.6 6.2 3.4 4.4 
 419 79 Normal tissue  6.7 5.2 3.6 6.3 
 431 64 Normal tissue  7.5 8.6 4.9 6.2 
 444 67 Normal tissue  6.5 6.1 2.6 4.8 
 446 42 Normal tissue  5.4 3.8 3.4 7.0 
 454 89 Normal tissue  7.0 5.1 3.4 8.0 
 469 69 Normal tissue  6.9 5.2 2.1 8.4 
 481 58 Normal tissue  7.4 7.6 3.9 7.1 
 483 80 Normal tissue  6.9 7.0 3.0 6.9 
 489 55 Normal tissue  7.9 5.3 2.9 7.7 
 493 92 Normal tissue  8.6 7.1 3.5 10.1 
 502 87 Normal tissue  7.5 7.4 1.3 9.6 
 504 78 Normal tissue  7.2 5.9 3.8 8.6 
 506 86 Normal tissue  8.6 9.6 3.5 10.0 
      Average 6.9 6.4 3.3 7.4 
Colorectal
Normal tissueSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 321 85 Normal tissue  6.0 6.4 4.5 6.2 
 328 73 Normal tissue  6.3 5.2 3.3 7.5 
 417 61 Normal tissue  4.6 6.2 3.4 4.4 
 419 79 Normal tissue  6.7 5.2 3.6 6.3 
 431 64 Normal tissue  7.5 8.6 4.9 6.2 
 444 67 Normal tissue  6.5 6.1 2.6 4.8 
 446 42 Normal tissue  5.4 3.8 3.4 7.0 
 454 89 Normal tissue  7.0 5.1 3.4 8.0 
 469 69 Normal tissue  6.9 5.2 2.1 8.4 
 481 58 Normal tissue  7.4 7.6 3.9 7.1 
 483 80 Normal tissue  6.9 7.0 3.0 6.9 
 489 55 Normal tissue  7.9 5.3 2.9 7.7 
 493 92 Normal tissue  8.6 7.1 3.5 10.1 
 502 87 Normal tissue  7.5 7.4 1.3 9.6 
 504 78 Normal tissue  7.2 5.9 3.8 8.6 
 506 86 Normal tissue  8.6 9.6 3.5 10.0 
      Average 6.9 6.4 3.3 7.4 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 418 61 Adenocarcinoma, invasive, moderately differentiated  6.3 6.1 4.8 5.6 
 420 79 Adenocarcinoma, moderately well differentiated  7.0 6.1 5.1 6.7 
 422 88 Adenocarcinoma, invading, moderately differentiated  7.3 10.0 8.6 2.2 
 432 64 Adenocarcinoma, poorly differentiated  7.7 12.1 6.6 9.6 
 439 65 Adenocarcinoma, moderately differentiated  5.5 6.0 7.0 7.7 
 445 67 Adenocarcinoma, moderately differentiated  6.4 8.4 8.1 8.8 
 447 42 Adenocarcinoma, moderately differentiated  4.8 4.0 5.3 7.5 
 455 89 Malignant neoplasm, lymphoma  9.1 7.7 5.3 12.6 
 470 69 Adenocarcinoma, mucinous  10.1 10.5 10.9 13.7 
 476 75 Adenocarcinoma  8.0 6.4 5.1 6.7 
 482 58 Adenocarcinoma, poorly differentiated  6.0 4.6 2.2 6.9 
 484 80 Adenocarcinoma, invasive  6.8 8.9 6.4 9.8 
 503 87 Adenocarcinoma, mucinous, moderately well differentiated  7.6 7.0 5.9 10.6 
 505 78 Adenocarcinoma, moderately differentiated  6.8 7.3 6.4 11.6 
 507 86 Adenocarcinoma, invasive, moderately differentiated  6.0 6.6 5.6 8.7 
      Average 7.0 7.4 6.3 8.6 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 418 61 Adenocarcinoma, invasive, moderately differentiated  6.3 6.1 4.8 5.6 
 420 79 Adenocarcinoma, moderately well differentiated  7.0 6.1 5.1 6.7 
 422 88 Adenocarcinoma, invading, moderately differentiated  7.3 10.0 8.6 2.2 
 432 64 Adenocarcinoma, poorly differentiated  7.7 12.1 6.6 9.6 
 439 65 Adenocarcinoma, moderately differentiated  5.5 6.0 7.0 7.7 
 445 67 Adenocarcinoma, moderately differentiated  6.4 8.4 8.1 8.8 
 447 42 Adenocarcinoma, moderately differentiated  4.8 4.0 5.3 7.5 
 455 89 Malignant neoplasm, lymphoma  9.1 7.7 5.3 12.6 
 470 69 Adenocarcinoma, mucinous  10.1 10.5 10.9 13.7 
 476 75 Adenocarcinoma  8.0 6.4 5.1 6.7 
 482 58 Adenocarcinoma, poorly differentiated  6.0 4.6 2.2 6.9 
 484 80 Adenocarcinoma, invasive  6.8 8.9 6.4 9.8 
 503 87 Adenocarcinoma, mucinous, moderately well differentiated  7.6 7.0 5.9 10.6 
 505 78 Adenocarcinoma, moderately differentiated  6.8 7.3 6.4 11.6 
 507 86 Adenocarcinoma, invasive, moderately differentiated  6.0 6.6 5.6 8.7 
      Average 7.0 7.4 6.3 8.6 
Esophagus
NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 477 76 Normal tissue  4.9 4.0 1.8 3.0 
 491 84 Normal tissue  9.1 9.4 4.7 10.3 
      Average 7.0 6.7 3.3 6.6 
Esophagus
NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 477 76 Normal tissue  4.9 4.0 1.8 3.0 
 491 84 Normal tissue  9.1 9.4 4.7 10.3 
      Average 7.0 6.7 3.3 6.6 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 478 76 Metastatic Adenocarcinoma, poorly differentiated  8.6 8.8 4.6 6.3 
 492 84 Squamous cell carcinoma, poorly differentiated  9.5 6.6 4.4 11.5 
      Average 9.0 7.7 4.5 8.9 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 478 76 Metastatic Adenocarcinoma, poorly differentiated  8.6 8.8 4.6 6.3 
 492 84 Squamous cell carcinoma, poorly differentiated  9.5 6.6 4.4 11.5 
      Average 9.0 7.7 4.5 8.9 
Kidney
NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 423 79 Normal tissue  9.7 7.0 5.1 4.9 
 425 61 Normal tissue  8.9 8.2 3.8 4.9 
 463 71 Normal tissue  8.1 3.0 2.1 5.5 
 467 47 Normal tissue  5.7 5.0 2.8 3.7 
 494 75 Normal tissue  7.1 6.5 4.1 7.8 
      Average 7.9 5.9 3.6 5.4 
Kidney
NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 423 79 Normal tissue  9.7 7.0 5.1 4.9 
 425 61 Normal tissue  8.9 8.2 3.8 4.9 
 463 71 Normal tissue  8.1 3.0 2.1 5.5 
 467 47 Normal tissue  5.7 5.0 2.8 3.7 
 494 75 Normal tissue  7.1 6.5 4.1 7.8 
      Average 7.9 5.9 3.6 5.4 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 464 71 Clear cell carcinoma (hypernephroma), well differentiated  14.0 8.7 7.5 8.6 
 468 47 Renal cell carcinoma  8.0 6.5 8.2 8.0 
 495 75 Renal cell carcinoma, chromophobe cell type  9.8 9.6 8.0 13.0 
 426 61 Renal cell carcinoma, papillary type     8.8 
      Average 10.6 8.3 7.9 9.6 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 464 71 Clear cell carcinoma (hypernephroma), well differentiated  14.0 8.7 7.5 8.6 
 468 47 Renal cell carcinoma  8.0 6.5 8.2 8.0 
 495 75 Renal cell carcinoma, chromophobe cell type  9.8 9.6 8.0 13.0 
 426 61 Renal cell carcinoma, papillary type     8.8 
      Average 10.6 8.3 7.9 9.6 
Lung
Normal tissueSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 415 66 Normal tissue  4.1 4.5 2.0 1.5 
 427 82 Normal tissue  4.2 4.8 3.1 1.8 
 450 57 Normal tissue  4.1 4.0 2.5 2.2 
 485 54 Normal tissue  4.4 5.0 2.9 3.7 
 487 70 Normal tissue  4.1 4.0 1.8 4.4 
 498 75 Normal tissue  6.5 5.1 2.1 2.6 
 510 72 Normal tissue  7.9 4.5 2.1 4.7 
      Average 5.0 4.6 2.4 3.0 
Lung
Normal tissueSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 415 66 Normal tissue  4.1 4.5 2.0 1.5 
 427 82 Normal tissue  4.2 4.8 3.1 1.8 
 450 57 Normal tissue  4.1 4.0 2.5 2.2 
 485 54 Normal tissue  4.4 5.0 2.9 3.7 
 487 70 Normal tissue  4.1 4.0 1.8 4.4 
 498 75 Normal tissue  6.5 5.1 2.1 2.6 
 510 72 Normal tissue  7.9 4.5 2.1 4.7 
      Average 5.0 4.6 2.4 3.0 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 414 68 Squamous cell carcinoma, poorly differentiated  9.5 7.7 5.3 8.0 
 416 66 Adenocarcinoma, moderately differentiated  8.6 9.4 5.9 6.6 
 428 82 Bronchiolo-alveolar carcinoma, non-mucinous type  7.1 7.1 5.7 7.2 
 451 57 Squamous cell carcinoma, poorly differentiated  8.5 8.3 8.7 10.5 
 456 61 Bronchiolo-alveolar adenocarcinoma  5.9 6.5 4.7 4.6 
 488 70 Squamous cell carcinoma, moderately differentiated  7.6 6.5 4.3 7.7 
 511 72 Bronchiolo-alveolar carcinoma, mucinous type  7.1 6.4 4.0 5.7 
      Average 7.8 7.4 5.5 7.2 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 414 68 Squamous cell carcinoma, poorly differentiated  9.5 7.7 5.3 8.0 
 416 66 Adenocarcinoma, moderately differentiated  8.6 9.4 5.9 6.6 
 428 82 Bronchiolo-alveolar carcinoma, non-mucinous type  7.1 7.1 5.7 7.2 
 451 57 Squamous cell carcinoma, poorly differentiated  8.5 8.3 8.7 10.5 
 456 61 Bronchiolo-alveolar adenocarcinoma  5.9 6.5 4.7 4.6 
 488 70 Squamous cell carcinoma, moderately differentiated  7.6 6.5 4.3 7.7 
 511 72 Bronchiolo-alveolar carcinoma, mucinous type  7.1 6.4 4.0 5.7 
      Average 7.8 7.4 5.5 7.2 
Ovary
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 490 55 Papillary serous carcinoma, metastatic to rectum  13.2 12.1 6.3 9.8 
 453 52 Granular cell, metastatic to bladder  6.4 3.6 7.2 4.8 
      Average 9.8 7.9 6.8 7.3 
Ovary
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 490 55 Papillary serous carcinoma, metastatic to rectum  13.2 12.1 6.3 9.8 
 453 52 Granular cell, metastatic to bladder  6.4 3.6 7.2 4.8 
      Average 9.8 7.9 6.8 7.3 
Stomach
NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 461 72 Normal tissue  6.8 6.0 3.3 5.7 
 496 69 Normal tissue  6.5 6.0 2.6 7.9 
      Average 6.7 6.0 3.0 6.8 
Stomach
NormalSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 461 72 Normal tissue  6.8 6.0 3.3 5.7 
 496 69 Normal tissue  6.5 6.0 2.6 7.9 
      Average 6.7 6.0 3.0 6.8 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 462 72 Adenocarcinoma, moderately differentiated  7.5 6.0 5.3 7.3 
 466 83 Infiltrating adenocarcinoma, moderate to poorly differentiated  7.2 4.9 3.1 9.0 
 497 69 Adenocarcinoma, moderately differentiated  6.0 4.4 3.7 7.0 
      Average 6.9 5.1 4.0 7.4 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 462 72 Adenocarcinoma, moderately differentiated  7.5 6.0 5.3 7.3 
 466 83 Infiltrating adenocarcinoma, moderate to poorly differentiated  7.2 4.9 3.1 9.0 
 497 69 Adenocarcinoma, moderately differentiated  6.0 4.4 3.7 7.0 
      Average 6.9 5.1 4.0 7.4 
Uterus
Normal tissueSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 457 72 Normal tissue  6.6 5.0 2.3 7.6 
Uterus
Normal tissueSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 457 72 Normal tissue  6.6 5.0 2.3 7.6 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 458 72 Adenocarcinoma, endometrium  8.5 7.9 5.7 8.8 
 474 70 Adenocarcinoma, endometrium, poorly differentiated  8.1 7.7 4.8 7.0 
      Average 8.3 7.8 5.3 7.9 
TumorSample no.SexRaceAgeHistologyPtcGliPDGFRαHip
 458 72 Adenocarcinoma, endometrium  8.5 7.9 5.7 8.8 
 474 70 Adenocarcinoma, endometrium, poorly differentiated  8.1 7.7 4.8 7.0 
      Average 8.3 7.8 5.3 7.9 
a

mRNA levels were measured by TaqMan analysis and normalized to the expression levels of GAPDH. Values in the table are ΔCT.

b

A, Asian; B, Black; H, Hispanic; W, White; U, Unknown.

We thank Bob Grant and Jerry Kropp, Gladstone Institute, San Francisco General Hospital, for assistance with TaqMan analysis.

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