Diagnostic Molecular Pathology最新文献

In breast cancer, the number of lymph node metastases is the strongest predictor of outcome. However, histopathology may underestimate the frequency of metastasis. Here we compare automated molecular detection of cytokeratin 19 mRNA by one-step nucleic acid amplification (OSNA) with histopathology of single tissue sections for the staging of axillary lymph nodes in patients with breast cancer. Axillary lymph nodes were collected from 55 patients with primary breast cancer and sentinel lymph node (SLN) metastases. The central 1-mm portion of each node was processed for hematoxylin-eosin staining, and the remaining tissue was analyzed by OSNA. According to OSNA, histopathology misclassified 41.8% of patients as negative for axillary node metastasis (P=0.007). Of the individual nodes considered negative by histopathology, 4.5% contained micrometastases and 2.5% contained macrometastases according to OSNA. Furthermore, 80% of micrometastases identified by histopathology were reclassified as macrometastases by OSNA. Histopathology failed to identify 81.1% of nodes shown to contain metastasis by OSNA. However, OSNA yielded no false-negative results. On the basis of OSNA results, 3 patients were reclassified to a higher pathologic stage. The number of SLN and non-SLN metastases was unrelated according to OSNA (P=0.891). These results show that, compared with molecular detection, histopathology of single tissue sections significantly underestimates the frequency of axillary node metastases. We discuss the implications of these findings in light of current recommendations on the staging of breast cancer.

Next-generation DNA and RNA sequencing requires intact nucleic acids from high-quality human tissue samples to better elucidate the molecular basis of cancer. We have developed a prostate biobanking protocol to acquire suitable samples for sequencing without compromising the accuracy of clinical diagnosis. To assess the clinical implications of implementing this protocol, we evaluated 105 consecutive radical prostatectomy specimens from November 2008 to February 2009. Alternating levels of prostate samples were submitted to Surgical Pathology as formalin-fixed, paraffin-embedded blocks and to the institutional biobank as frozen blocks. Differences in reported pathologic characteristics between clinical and procured specimens were compared. Clinical staging and grading were not affected by the biobank protocol. Tumor foci on frozen hematoxylin and eosin slides were identified and high-density tumor foci were scored and processed for DNA and RNA extractions for sequencing. Both DNA and RNA were extracted from 22 cases of 44 with high-density tumor foci. Eighty-two percent (18/22) of the samples passed rigorous quality control steps for DNA and RNA sequencing. To date, DNA extracted from 7 cases has undergone whole-genome sequencing, and RNA from 18 cases has been RNA sequenced. This protocol provides prostate tissue for high-throughput biomedical research and confirms the feasibility of actively integrating prostate cancer into The Cancer Genome Atlas Program, a member of the International Cancer Genome Consortium.

Monoclonal therapies could represent baseline-personalized medicine for patients with neoplasia. One of the most successful examples is Trastuzumab, a humanized antibody against epidermal growth factor receptor 2. Human epidermal growth factor receptor 2 (HER2) is a trans-membrane tyrosine kinase coded by the gene HER2/neu and overexpressed in approximately 12% to 20% of infiltrating breast carcinomas. The overexpression of HER2 is an independent adverse prognostic factor in relation to survival and is also predictive of response to treatment. Therefore, the correct evaluation of HER2 status is essential for the management of infiltrating breast carcinoma to determine the response to Trastuzumab. The most common evaluation technique is immunohistochemistry, which is confirmed by fluorescent or chromogenic monochrome or dual-gene in situ hybridization in ambiguous cases (immunohistochemical 2+). Our objective was to evaluate the diagnostic value of a new technique on the basis of HER2 mRNA in situ hybridization (HistoSonda) and study its correlation with immunohistochemistry and dual-chromogenic in situ hybridization (DUO-CISH) in 403 cases of infiltrating breast carcinoma. The percentage of DUO-CISH amplification was 25.8%, HistoSonda positivity was 31.2%, and positivity for Hercep-Test was 48.1%, including (+2) and (+3). Comparisons were made of each of the techniques, HistoSonda to IHQ and HistoSonda to DUO-CISH. The overall concordance between DUO-CISH and HistoSonda was 89%. Our data support the consistency of HistoSonda as a useful tool to determine HER2 status in breast cancer.

Formalin-fixed paraffin-embedded tissue (FFPET) samples are a potential source of DNA for molecular epidemiological studies. However, the use of FFPET samples can be restricted by the yield and quality of DNA isolated. The aim of this study was to examine whether FFPET biopsies from pediatric central nervous system tumors were a feasible alternative to archival frozen tissue when characterizing common gene polymorphisms. DNA was isolated from 50 frozen pediatric central nervous system tumor biopsies and matched FFPET samples. Real-time polymerase chain reaction (PCR) was used to quantify DNA and characterize GSTT1, GSTM1, GSTP1, and MTHFR gene polymorphisms. The use of whole-genome amplification (WGA) to increase DNA yields was also investigated. The results showed that DNA isolated from FFPET samples was more fragmented and provided smaller yields than DNA isolated from frozen samples. Attempts to increase the DNA yield from FFPET using WGA were unsuccessful. DNA from FFPET samples was successfully genotyped for the GSTP1 Ile105Val and MTHFR 677 C>T polymorphisms in 98% of samples and was 100% concordant with the results from frozen tissue. However, DNA from FFPET performed poorly in real-time PCR assays for GSTM1 and GSTT1 deletion polymorphisms. Our investigations show that DNA extracted from FFPET is substantially fragmented and not readily amplified using WGA. In addition, careful validation of PCR assays should be carried out due to the variable amplification of fragmented FFPET DNA.

Due to the approval of various new targeted therapies for the treatment of cancer, molecular pathology laboratories with a diagnostic focus have to meet new challenges: simultaneous handling of a large number of samples, small amounts of input material, and fragmentation of nucleic acids because of formalin fixation. As a consequence, fully automated systems for a fast and standardized extraction of high-quality DNA from formalin-fixed paraffin-embedded (FFPE) tissues are urgently needed. In this study, we tested the performance of a fully automated, high-throughput method for the extraction of nucleic acids from FFPE tissues. We investigated the extraction performance in sections of 5 different tissue types often analyzed in routine pathology laboratories (cervix, colon, liver, lymph node, and lung; n=340). Furthermore, we compared the quality, labor input, and applicability of the method for diagnostic purposes with those of a laboratory-validated manual method in a clinical setting by screening a set of 45 colorectal adenocarcinoma for the KRAS mutation. Automated extraction of both DNA and RNA was successful in 339 of 340 FFPE samples representing 5 different tissue types. In comparison with a conventional manual extraction protocol, the method showed an overall agreement of 97.7% (95% confidence interval, 88.2%-99.9%) for the subsequent mutational analysis of the KRAS gene in colorectal cancer samples. The fully automated system is a promising tool for a simple, robust, and rapid extraction of DNA and RNA from formalin-fixed tissue. It ensures a standardization of sample processing and can be applied to clinical FFPE samples in routine pathology.

Objective: The aim of this study was to determine the impact of standard methods for processing decalcified highly mineralized tissues on RNA yield and quality from microdissected samples.

Design: Rat mandibles were fixed with either formalin-based or ethanol-based fixatives, decalcified in 20% ethylenediaminetetraacetic acid solution for 15 days, and embedded in paraffin. Transversal sections of the molars were mounted on membrane glass slides for laser capture microdissection. Unfixed frozen liver samples were used as controls to determine the impact of fixatives, decalcification and paraffin embedding on RNA integrity and recovery after sample preparation, and laser microdissection. Total RNA was obtained from periodontal ligament and fresh-frozen liver; RNA quality was assessed by Bioanalyzer, and 5 ng of total RNA was used for cDNA synthesis followed by gene expression analyses by polymerase chain reaction using 3 sets of primers for glyceraldehyde 3-phosphate dehydrogenase.

Results: Data analysis demonstrated that all fixed samples presented some level of RNA fragmentation as compared with fresh-frozen samples (P<0.05). Samples fixed with Protocol (10% formalin) showed the least RNA fragmentation as compared with other fixatives (P<0.05), and biologically useful RNA was extracted even from microdissected samples with a minimum RNA Integrity Number of 1.5. Moreover, RNA fragments up to 396 bp were assayable by reverse transcriptase-polymerase chain reaction, although short-targeted fragments as 74 bp were more consistently amplified.

Conclusions: Although variable levels of RNA fragmentation should be expected, gene expression analysis can be performed from decalcified paraffin-embedded microdissected samples, with the best results obtained for short-targeted fragments around 70 bp.

Her-2/neu gene amplification is an established prognostic factor in breast cancer, and Her-2/neu protein is the target of the therapeutic monoclonal antibody Herceptin. More recently, topoisomerase IIα became a new focus of breast cancer research because of its role as a target for anthracycline therapy. Therefore, we compared Her-2/neu and topoisomerase IIα amplification/deletion in a large series of advanced breast cancer using fluorescence in situ hybridization. Paraffin-embedded archival tissue from 245 patients was retrieved and assessed for Her-2/neu and topoisomerase IIα amplification/deletion by fluorescence in situ hybridization according to standard protocols. Relation to clinical data and survival was sought. A total of 245 cases were analyzed. Amplification for Her-2/neu was seen in 57 cases (23.3%), and for topoisomerase IIα in 12 cases (4.9%). Coamplification was found in 9 samples (3.7%), 3 cases (1.2%) showed amplification of topoisomerase IIα but not of Her-2/neu, and 48 samples (19.8%) displayed amplification for Her-2/neu but not for topoisomerase IIα. Correlation to the histologic type, the stage, or the grade could not be found. Only the amplification of topoisomerase IIα was associated with very poor outcome; survival of cases with amplification of Her-2/neu only was slightly lower than the mean overall survival (27.4 vs. 31.9 mo). Amplification of Her-2/neu and/or topoisomerase IIα is associated with poor overall survival. Amplification of topoisomerase IIα does not seem to be necessarily linked to Her-2/neu-amplification. However, independent determination of these 2 markers seems to be valuable for an individualized therapy of breast cancer patients.

Biomarkers that facilitate prediction of disease progression in lung cancer patients might be clinically valuable in optimizing individualized therapy. In this study, the ability of the DNA methylation biomarkers PITX2 and SHOX2 to predict disease outcome in lung cancer patients has been evaluated. Quantitative, methylation-specific (HeavyMethyl), real-time polymerase chain reaction assays were used to measure DNA methylation of PITX2 and SHOX2 in bisulfite-converted DNA from formalin-fixed, paraffin-embedded tissues from 474 non-small-cell lung cancer patients. In univariate Cox Proportional Hazard analysis, high methylation of SHOX2 and PITX2 was a significant predictor of progression-free survival [SHOX2: n=465, hazard ratio (HR)=1.395 (1.130 to 1.721), P=0.002; PITX2: n=445, HR=1.312 (1.059 to 1.625), P=0.013]. Patients with low methylation of either PITX2 and/or SHOX2 (n=319) showed a significantly higher risk of disease progression as compared with patients with higher methylation of both genes [n=126; HR=1.555 (1.210 to 1.999), P=0.001]. This was particularly true for the subgroup of patients receiving no adjuvant radiotherapy or chemotherapy [n=258, HR=1.838 (1.252 to 2.698), P=0.002]. In multivariate analysis, both biomarkers added significant independent prognostic information to pT, pN, pM, and grade. Another interesting finding of this study was that SHOX2 and PITX2 DNA methylation was shown to be inversely correlated with TTF1 (also known as NKX2-1) expression (PITX2: P=0.018, SHOX2: P<0.001). TFF1 expression was previously found to be associated with improved survival in the same patient cohort. DNA methylation of PITX2 and SHOX2 is an independent prognostic biomarker for disease progression in non-small-cell lung cancer patients.

Aberrant hypermethylation of CpG islands (CGIs) in hMLH1 promoter regions has been well known to play an important role in the tumorigenesis of human sporadic colorectal carcinoma (SCRC). In this study, bisulfite sequencing was performed to analyze the methylation variable positions (MVPs) profiles of hMLH1 promoter CGIs in 30 clinical SCRC patients, and further analysis was carried out to evaluate the associations between the CGI methylation and the clinicopathological features in SCRC. Among the 2 CGIs in the hMLH1 promoter, that is, CGI-I and CGI-II, 20% (6/30) and 13% (4/30) of the patients had methylated CGI-I and CGI-II, respectively. Suppressed expression of hMLH1was significantly correlated with methylation of CGI-I but not CGI-II. Further analysis of the MVP profiles of CGI-I showed that most of the MVPs were hypermethylated and others were poorly methylated or unmethylated. The profiles could be classified into at least 4 groups based on the methylation status of 3 MVPs at positions 21 to 23 in CGI-I. All 6 patients with methylated CGI-I belonged to group I. This result suggests that the above 3 MVPs in CGI-I should be a targeted region to further analyze the epigenetic features of hMLH1 in human SCRC. Our results further suggest that MVP profiling is useful for identifying the aberrantly methylated CGIs associated with suppressed gene expression.

Melanomas frequently harbor BRAFV600 mutations. Vemurafenib (RG7204/PLX4032), a small-molecule inhibitor of mutant BRAF, has shown striking clinical efficacy in BRAFV600 mutant melanoma, creating the need for a well-validated companion diagnostic to select patients for treatment. We describe analytic performance characteristics of the cobas 4800 BRAF V600 Mutation Test, the test used to select patients for the pivotal vemurafenib trials. This real-time polymerase chain reaction assay was designed to detect the V600E (1799T>A) mutation DNA from formalin-fixed paraffin-embedded tissue samples. Sensitivity was assessed using blends of cell lines or tumor DNA, and tumor specimens with low levels of mutant alleles, as determined by 454 sequencing (a quantitative next-generation pyrosequencing method). A >96% hit rate was obtained across all specimen types with 5% mutant alleles at a DNA input of 125 ng, an amount readily obtained from one 5-μm section. The cobas test showed a higher sensitivity and specificity than direct bidirectional sequencing in a panel of 219 melanoma specimens. Cross reactivity with V600K and V600D was observed. Repeated testing of 5 specimens by 2 operators, using different instruments and reagent lots, yielded correct calls in 158/160 tests (98.8%). A set of 26 highly pigmented samples were identified that gave invalid test results. A simple 1:2 dilution resulted in a valid test result of 76% in such cases. The cobas test is a reproducible assay that detects some non-V600E mutations and is more accurate than direct sequencing in detecting BRAFV600E.