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Imaging, Diagnosis, Prognosis |
Authors' Affiliations: 1 Molecular Diagnostic Laboratory, Department of Clinical Biochemistry; Departments of 2 Urology and 3 Theoretical Statistics, Aarhus University Hospital, Skejby, Denmark; 4 Institut Municipal d'Investigació Mèdica and 5 Center for Research in Environmental Epidemiology, Universitat Pompeu Fabra, Barcelona, Spain; 6 Hospital Universitario de Elche, Elche, Spain; 7 Cancer Research UK Clinical Centre and 8 Pyrah Department of Urology, St James's University Hospital, Leeds, England; Departments of 9 Urology and 10 Genetics and Pathology, University Hospital, Uppsala, Sweden; 11 Hôpital Henri Mondor, Créteil, France; 12 Oncologie Moléculaire, UMR144, Centre National de la Recherche Scientifique, Institut Curie, Paris, France; and 13 Department of Clinical Pathology, Odense University Hospital, Denmark
Requests for reprints: Torben F. Ørntoft, Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, Denmark. Phone: 45-89495100; Fax: 45-89496018; E-mail: orntoft{at}ki.au.dk.
| Abstract |
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Experimental Design: We analyzed tumors from 404 patients diagnosed with bladder cancer in hospitals in Denmark, Sweden, England, Spain, and France using custom microarrays. Molecular classifications were compared with pathologic diagnosis and clinical outcome.
Results: Classification of disease stage using a 52-gene classifier was found to be highly significantly correlated with pathologic stage (P < 0.001). Furthermore, the classifier added information regarding disease progression of Ta or T1 tumors (P < 0.001). The molecular 88-gene progression classifier was highly significantly correlated with progression-free survival (P < 0.001) and cancer-specific survival (P = 0.001). Multivariate Cox regression analysis showed the progression classifier to be an independently significant variable associated with disease progression after adjustment for age, sex, stage, grade, and treatment (hazard ratio, 2.3; P = 0.007). The diagnosis of CIS using a 68-gene classifier showed a highly significant correlation with histopathologic CIS diagnosis (odds ratio, 5.8; P < 0.001) in multivariate logistic regression analysis.
Conclusion: This multicenter validation study confirms in an independent series the clinical utility of molecular classifiers to predict the outcome of patients initially diagnosed with nonmuscle-invasive bladder cancer. This information may be useful to better guide patient treatment.
The nonmuscle-invasive tumors account for
75% of newly diagnosed cases. A low proportion of patients are cured after tumor resection, but the tumors of more than 60% of these patients recur, and the frequency of recurrences has a significant effect on the patients' quality of life. Some of these patients also develop muscle-invasive tumors over time, the proportion ranging from very low for noninvasive papillary low-grade tumors to up to 60% progression for high-grade submucosa-invasive tumors (2, 3). Clinical risk factors for progression include invasion of the lamina propria, high grade, tumor size, occurrence of carcinoma in situ (CIS), and multiplicity or recurrence of high-risk tumors. The recurrence of nonmuscle-invasive tumors may be prevented by intravesical instillations of Bacillus Calmette-Guerin (BCG) or, for example, mitomycin-C chemotherapy. BCG is also used to treat patients with CIS lesions that, if not treated, progress to muscle-invasive disease in 50% of cases (2). The treatment is effective in about 70% of the cases but has common side effects of local pain and dysuria. Cystectomy may be considered in selected cases of patients with very frequent recurrences, stage pT1, high-grade lesions, CIS, and failure of BCG treatment. Radical treatment is, however, a major surgical procedure, with postoperative morbidity and effect on the patients' quality of life. Presently, no molecular markers exist that can guide the clinicians in the selection of treatment regimens for patients with nonmuscle-invasive bladder cancer.
The advent of genome-wide transcriptome profiling has had a big effect on the discovery rate of new molecular markers or gene expression signatures for classifying and predicting disease outcome in various cancers, including bladder cancer (48). Previously, we have used Affymetrix GeneChips to identify expression signatures of potential clinical value. First, we identified a gene expression signature for classifying tumor samples according to disease stage (Ta, T1, and T2-T4). That study also included the identification of a gene signature for predicting recurrence frequency in nonmuscle-invasive tumors (9). In a later study, we identified a gene signature for classifying early-stage bladder tumors according to the presence of surrounding CIS (10). Finally, we have identified a gene signature for predicting disease progression (11). Only few studies have thus far documented a clinical utility of the identified gene expression signatures through large-scale validation in independent tumor series. In this study, we have validated the diagnostic and prognostic value of these four gene signatures in an independent series of tumors from a cohort of 404 patients diagnosed with bladder cancer in hospitals in Denmark, Sweden, France, England, and Spain. This study confirms in an independent series the clinical utility of molecular classifiers for diagnosis and prognosis of patients initially diagnosed with nonmuscle-invasive bladder cancer.
| Materials and Methods |
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Treatment and follow-up information. The samples were taken from patients that were operated in the years 1987 to 2000 in hospitals in Denmark, Sweden, Spain, France, and England. Ninety-four patients received intravesical treatment with BCG or mitomycin-C. Progression of the disease was defined as (a) invasion into the bladder muscle, verified by microscopy; or (b) more distant metastases verified also by microscopy except for rare cases where this was not possible, but where scanning revealed an unambiguous metastasis. Twenty-one patients with nonmuscle-invasive tumors were cystectomized before progression occurred and 15 patients after progression. Twenty patients with primary muscle-invasive cancer were cystectomized. Progression-free survival time was recorded from sampling visit and censored at the time of the last control cystoscopy or at cystectomy. Disease-specific survival was recorded from sampling visit and censored at the time of the last annotation of the patient being alive, and death causes were obtained by a review of the hospital files. The follow-up was done retrospectively, and we included as many tumors form the different centers as possible, preferably high-risk tumors. Consequently, the material used in this study is selected and does not reflect the tumor group sizes that would be included from a prospective study. Details on clinical courses are outlined in Supplementary File 1. The high and low clinical risk groups used were defined as high clinical risk (stage T1 or high grade or CIS) and other tumors (low risk; ref. 13).
RNA extraction and quality control. RNA was extracted from the Danish and English samples using a standard Trizol RNA extraction method (Invitrogen). RNA from Swedish and Spanish samples was extracted using RNeasy mini kit (Qiagen), and RNA from the French samples was extracted by cesium chloride density centrifugation (14). All RNA was quality controlled using an Agilent Bioanalyzer (criteria: 28S/18S >1 and RIN>5).
Gene expression profiling. For the validation of the gene signatures, a microarray platform was developed, including probes for the genes comprised in the four expression signatures previously described. Oligonucleotide design, microarray spotting procedure, sample labeling, array hybridization, and scanning were done as previously described (11). Briefly, all classifier genes were represented by one to four 60-mer oligonucleotides spotted in duplicate on CodeLink slides (GE Health Care), and all samples (N = 404) were assayed twice using the microarrays. One microgram total RNA from each tumor was reversed transcribed to cDNA using an oligo-dT primer containing a T7 RNA polymerase promoter sequence. The cDNA was transcribed into cRNA with incorporation of aminoallyl-linked UTP nucleotides for Cy dye binding. All tumor cRNA samples were labeled with Cy3 and analyzed against a common reference sample (Universal Human Reference RNA, Stratagene) labeled with Cy5. TIGR spotfinder 2.23 software was used to generate raw-intensity data, which were Lowess (blockwise) normalized using TIGR MIDAS 2.19 software (15). Average log 2 ratios were calculated from the normalized data based on the four measurements of each gene. Microarray data are available at GEO14 with series accession no. GSE5479.
Probe selection and classification procedures. For stage classification, we previously identified 79 genes, and for recurrence classification, a set of 26 genes (9). For CIS classification, we previously identified a 16-gene signature and furthermore delineated the 100 best marker genes (10). For progression classification, we identified a 45-gene signature and, in addition, delineated the 200 best marker genes (11). In this study, we focused on all previously reported classifier genes and did not focus solely on the previously reported optimal signatures for the classifiers. The optimal gene expression signatures were identified previously based on cross-validation performance using a limited number of training samples. This procedure may result in very different numbers of "optimal" gene signatures, depending on the number of training samples used. We only excluded previously identified genes when the probes did not work on the new platform. Therefore, this new gene selection approach applied in this work resulted in different optimal gene expression signatures than reported in the original studies, but no new genes were introduced. Genes used in previously reported optimal gene signatures are listed in Supplementary File 2. Oligonucleotides of sequences representing the genes were spotted on the microarray, and in this study, we included all genes in the classifiers that showed a Pearson correlation equal to or above 0.25 when expression levels were compared with previously generated Affymetrix GeneChip gene expression intensities for the same samples. The probe with highest Pearson correlation was selected when several probes for the same gene were above the correlation threshold. This gene re-selection on the new array platform generated a 52-gene stage classifier, a 68-gene CIS classifier, a 20-gene recurrence classifier, and a 88-gene progression classifier. Only samples previously used for generating the classifier gene sets were used in the selection of best-performing genes on the new platform. Samples used for probe selection were not used for validation purposes. The probes used in the classifiers are shown in Supplementary File 2.
Maximum likelihood classifiers were constructed as previously described (9). Because the classifiers were initially identified using the Affymetrix GeneChip platform, the classifier group mean values were regenerated by training the classifiers with samples previously profiled on the Affymetrix platform (stage classifier, n = 18; recurrence classifier, n = 19; CIS classifier, n = 16; progression classifier, n = 15; see Supplementary File 1 for details on samples used for training). Of importance, none of the samples used to generate the classifiers were included in the validation set. In total, we profiled 404 tumors that all were used as independent test samples for one or more classifier validations. All microarray measurements were done blinded to patient diagnosis and outcome. We used the following patient selection criteria for testing the different classifiers: Out of the 404 tumors, we included 386 for stage classifier validation. The remaining 18 samples that were used for training the stage classifier were used for validation of other classifiers. Samples used to validate the CIS classifier are pTa and pT1 tumors from patients with known CIS status from either routine random biopsies taken at all visits to the clinic (at least two biopsies with CIS), or when CIS was diagnosed in the diagnostic sections from the analyzed tumor. Samples used to validate the recurrence classifier are pTa tumors with short recurrence frequency (<8 months) or at least 24-month recurrence-free survival (criteria used in the original study). Only samples from Danish patients were used. Samples used to validate the progression classifier were only samples from patients with pTa and pT1 tumors with no previous or synchronous muscle-invasive tumors.
Statistical procedures. Kaplan-Meier estimates, univariate and multivariate Cox regression analyses, and logistic regression analyses were done using the STATA 8.0 statistical analysis software.
| Results |
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2 test). Tumors classified as muscle invasive (stage T2-T4) had significantly lower cancer-specific survival times (Fig. 1A
; log-rank test, P < 0.001). The stage classifiers ability to predict future stage progression of nonmuscle-invasive bladder tumors reported in our original study was confirmed as well (Fig. 1B; log-rank test, P < 0.001; ref. 9). The previously published 26-gene signature for recurrence prediction showed no significant correlation to clinical outcome (results not shown).
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20%; this includes low-grade Ta tumors with high-risk molecular profile as well as T1 and grade 3 tumors with low-risk molecular profile. Molecular classification could also be used to guide treatment decisions based on the inclusion of exclusively those patients with a high classification power, eliminating those where classification is weak. We calculated the sensitivity and specificity of the progression classifier for different tail percentiles (Supplementary Fig. S2) and found, for example, for the 50% fraction of patients classified with highest strength that the sensitivity and specificity for progression prediction was 83% and 65%, respectively.
CIS classifier validation. Molecular classification of CIS was done using a 68-gene signature for the 150 patients with known CIS status (Fig. 2B). The CIS classifier correctly classified 36 of 45 samples with CIS (80% sensitivity) and correctly classified 71 of 105 with no CIS (68% specificity). These results were independent of age, sex, disease stage, and grade in multivariate logistic regression analysis (odds ratio 5.78; 95% confidence interval, 2.25-14.88; P < 0·001, Table 3 ). As CIS is associated with a high risk of disease progression, the signature can also be considered as a progression risk signature. When using the CIS signature to predict progression for all patients with nonmuscle-invasive tumors and available follow-up (n = 294), we obtained a sensitivity of 75% and a specificity of 55% with positive and negative predictive values of 28% and 90%, respectively.
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| Discussion |
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All patients in the study were treated with transurethral resection of tumors and, in many cases, intravesical BCG or mitomycin-C treatment. Consequently, predictive classifiers are superimposed with treatment, and this obscures the outcome and makes end point monitoring difficult. This fact may explain the relatively low specificity for the progression classifier. In this work, we have exclusively used zero as cutoff point between the classifier groups. However, other cutoff points could be used to, for example, increase the sensitivity of the test.
The classifiers for progression and CIS were developed using different Affymetrix gene expression microarrays and with different individual tumors. This is probably the reason that the published gene profiles show little overlap, although outcome variables are highly correlated. This has also been stressed in previous studies (1719). As we showed here, the classification results may be improved by combining different signatures. A three-way approach was shown to define a high-risk group, a low-risk group, and an intermediate-risk group of patients. This approach is more related to the conventional way of clinical decision making; however, it showed a very high specificity. Future work will hopefully further enhance the performance of molecular diagnosis and risk prediction.
We showed the clinical benefit of applying the classifiers because molecular classification proved capable of improving clinical diagnosis and risk prediction. Molecular CIS diagnosis is also of outmost importance because the diagnosis of CIS is difficult as not all clinicians take random biopsies for CIS diagnosis, the number of biopsies varies, and the diagnosis may be associated with sampling error. Hence, we believe that this study represents an important step towards the clinical use of molecular diagnosis in bladder cancer. Further evaluation of the molecular risk prediction in prospective, standardized setting is warranted and will hopefully open up the way to broader use of these molecular signatures in routine clinical analysis. In a potential clinical use of the RNA-based signatures, it is imperative to establish good standard operating procedures to secure a good RNA quality. Finally, we conclude that the results of this European multicenter study for validation of previously reported gene expression signatures have proved the value of the classifiers for especially progression and CIS classification. The study documents the clinical utility of applying molecular classifiers to guide the decision for treatment regimen for patients initially diagnosed with nonmuscle-invasive bladder cancer.
| Acknowledgments |
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| Footnotes |
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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.
Note: Supplementary data for this article are available at Clinical Cancer Research Online (http://clincancerres.aacrjournals.org/).
14 http://www.ncbi.nlm.nih.gov/geo/ ![]()
Received 12/12/06; revised 2/ 7/07; accepted 3/22/07.
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