An approach to the validation of novel molecular markers of breast cancer via TMA-based FISH scanning

State-of-the-art FISHing: automated analysis of cytogenetic aberrations in interphase nuclei

Interphase fluorescence in situ hybridization (i-FISH) is a powerful tool for visualizing various molecular targets in non-dividing cells. Manual scoring of i-FISH signals is a labor intensive, time-consuming, and error-prone process liable to subjective interpretation. Automated evaluation of signal patterns provides the opportunity to overcome these difficulties. The first report on automated i-FISH analysis has been published 20 years ago and since then several applications have been introduced in the fields of oncology, and prenatal and fertility screening. In this article, we provide an insight into the automated i-FISH analysis including its course, brief history, clinical applications, and advantages and challenges. The lack of guidelines for describing new automated i-FISH methods hampers the precise comparison of performance of various applications published, thus, we make a proposal for a panel of parameters essential to introduce and standardize new applications and reproduce previously described technologies.

Outcome of patients with early-stage breast cancer treated with doxorubicin-based adjuvant chemotherapy as a function of HER2 and TOP2A status

PURPOSE

Amplification and deletion of the TOP2A gene have been reported as positive predictive markers of response to anthracycline-based therapy. We determined the status of the HER2 and TOP2A genes in a large cohort of breast cancer patients treated with adjuvant doxorubicin (A) and cyclophosphamide (C).

PATIENTS AND METHODS

TOP2A/CEP17 and HER2/CEP17 fluorescent in situ hybridization (FISH) were performed on tissue microarrays (TMAs) constructed from 2,123 of the 3,125 women with moderate-risk primary breast cancer who received equivalent doses of either concurrent adjuvant chemotherapy with A plus C (n = 1,592) or sequential A followed by C (n = 1,533).

RESULTS

An abnormal TOP2A genotype was identified for 153 (9.4%) of 1,626 patients (4.0% amplified; 5.4% deleted). An abnormal HER2 genotype was identified for 303 (20.4%) of 1,483 patients (18.8% amplified; 1.6% deleted). No significant differences in either overall survival (OS) or disease-free survival (DFS) were identified for TOP2A. In univariate analysis, OS and DFS rates were strongly and adversely associated only with higher levels of HER2 amplification (ratio > or = 4.0). Survival was not associated with low-level HER2 amplification (ratio > or = 2; OS hazard ratio [HR], 1.14; P = .39; DFS HR, 1.07; P = .62), but it was associated for a ratio > or = 4 (OS HR, 1.45; P = .03; DFS HR, 1.38; P = .033), in which analysis was adjusted for menopausal status, hormone receptor status, treatment, number of positive nodes, and tumor size.

CONCLUSION

In this population of patients with early-stage breast cancer who were treated with adjuvant AC chemotherapy, TOP2A abnormalities were not associated with outcome. HER2 high-level amplification was a prognostic marker in anthracycline-treated patients.

Virtual microscopy as an enabler of automated/quantitative assessment of protein expression in TMAs

Tissue Microarrays facilitate high-throughput immuohistochemistry; however, there are key bottlenecks apparent in their analysis, particularly when conducting microscope-based manual reviews. Traditionally Tissue Microarray assessments were performed using a microscope where results were either transcribed or dictated and subsequently entered into flat-file spreadsheets. This process is labour intensive, prone to error and negates the advantages of the high-throughput Tissue Microarray format. In addition, human interpretations of staining intensity parameters are highly subjective and therefore prone to inter- and intra-observer variability. The advent of Virtual Slides has permitted the review of tissue slides across the Internet. In addition, this new technology enables the creation of software solutions to assist in the manual and automated review of Tissue Microarrays, through the use of computer aided image analysis. There are numerous academically developed and commercially available applications which assist in Tissue Microarray reviews; functionality of these systems range in complexity and application domains. The review which follows describes these systems and outlines technical considerations to be assessed when deciding on a Tissue Microarray workflow solution.

Quantification of diverse subcellular immunohistochemical markers with clinicobiological relevancies: validation of a new computer-assisted image analysis procedure

Tissue microarray technology and immunohistochemical techniques have become a routine and indispensable tool for current anatomical pathology diagnosis. However, manual quantification by eye is relatively slow and subjective, and the use of digital image analysis software to extract information of immunostained specimens is an area of ongoing research, especially when the immunohistochemical signals have different localization in the cells (nuclear, membrane, cytoplasm). To minimize critical aspects of manual quantitative data acquisition, we generated semi-automated image-processing steps for the quantification of individual stained cells with immunohistochemical staining of different subcellular location. The precision of these macros was evaluated in 196 digital colour images of different Hodgkin lymphoma biopsies stained for different nuclear (Ki67, p53), cytoplasmic (TIA-1, CD68) and membrane markers (CD4, CD8, CD56, HLA-Dr). Semi-automated counts were compared to those obtained manually by three separate observers. Paired t-tests demonstrated significant differences between intra- and inter-observer measurements, with more substantial variability when the cellular density of the digital images was > 100 positive cells/image. Overall, variability was more pronounced for intra-observer than for inter-observer comparisons, especially for cytoplasmic and membrane staining patterns (P < 0.0001 and P = 0.050). The comparison between the semi-automated and manual microscopic measurement methods indicates significantly lower variability in the results yielded by the former method. Our semi-automated computerized method eliminates the major causes of observer variability and may be considered a valid alternative to manual microscopic quantification for diagnostic, prognostic and therapeutic purposes.

Successful application of a direct detection slide-based sequential phenotype/genotype assay using archived bone marrow smears and paraffin embedded tissue sections

Identification of genetic abnormalities in pathological samples is critical for accurate diagnosis, risk stratification, detection of minimal residual disease, and assessment of response to therapy. Interphase fluorescence in situ hybridization analysis is the standard cytogenetic assay used by many laboratories to detect specific clonal karyotypic aberrations in formalin-fixed, paraffin-embedded tissue. However, direct correlation with immunophenotype or morphology in individual cells is rarely performed because the procedural steps are labor intensive and usually require extensive troubleshooting. In this study, we present a sequential fluorescence in situ hybridization-based technique that uses the identical archived bone marrow smears or paraffin-embedded tissue sections previously evaluated by a pathologist for morphological or immunohistochemical characteristics. This approach is relatively straightforward, using uncomplicated pretreatment and hybridization conditions and basic equipment attached to an automated image analyzer with image capture software to record the location of targeted cells for genotypic/phenotype correlation. Furthermore, the method has proved reliable and reproducible on test samples regardless of specimen age, tissue type, or referring institution.

Genotyping of phenotypically defined cells in neoplasia: enhanced immunoFISH via tyramide signal amplification (TSA) segregates immunophenotypically-defined cell populations for gated genotyping

Molecular morphologic tools exist for simultaneously visualizing immunophenotype and genotype of tumors, but are frequently hampered by a delicate balance between removing sufficient amount of the protein blocking full access of the probe to hybridize to target nucleic acids while still preserving sufficient target antigen for immunophenotyping. The result is often suboptimal, with either insufficiently visualized gene deletions and amplifications due to masking protein, or overdigestion of the protein target. Our purpose was to design and validate a gated genotyping assay that enables optimal and concomitant detection of both gene and protein. Using the proliferating endothelial cell compartment within gliomas organized in a tissue microarray (TMA), we tested the hypothesis that tyramide signal amplification (TSA) with deposition of a fluorochrome could be used during immunophenotyping, permitting sufficient protein digestion while insuring probe accessibility to nucleic acid target. The method was successfully validated using a TMA containing 38 glioma cases previously genotyped for EGFR amplification. CD31 positive endothelial cells were segregated via TSA-based Alexa-Fluor 647 immunofluorescence for analysis of EGFR amplification of the gliomas organized in the TMA. Enhanced immunoFISH (TSA) successfully segregates immunophenotypically-defined cell populations for gated genotyping.

The specificity of interphase FISH translocation probes in formalin fixed paraffin embedded tissue sections is readily assessed using automated staining and scoring of tissue microarrays constructed from murine xenografts

Implementation of interphase fluorescence in situ hybridization (FISH) assays in the clinical laboratory requires validation against established methods. Validation tools in common use include exchange of consecutive sections with another institution that has already established the FISH assay, comparison with conventional banded metaphase cytogenetics, confirmation of specificity using probed normal metaphases, consecutive paraffin sections of a validation set tested by a reference laboratory, and specificity assessment against well characterized cell lines. We have investigated the feasibility of using tissue microarrays (TMA) constructed from murine xenografts as a preliminary specificity-screening tool for validation of interphase FISH assays. Cell lines currently in use for FISH controls are used to generate xenografts in SCID mice which are fixed in formalin and paraffin embedded. A TMA is constructed using duplicate donor cores from the xenograft blocks. Xenografts used represent a wide range of translocations used routinely for formalin fixed paraffin embedded sections evaluated by FISH. Probe cocktails (Abbott-Vysis), for several non-random translocations associated with hematologic neoplasms and soft tissue sarcomas have been used in this manner. On-line deparaffinization, cell conditioning, and prehybridization steps are automated using a staining workstation (Ventana Discovery XT); hybridization and stringency washes are performed manually offline. FISH-probed TMAs are tracked using a Metasystems image scanner and analyzed using classifiers specifically developed for each molecular abnormality. FISH results for each xenograft in the TMA correspond exactly to the genotype previously established for the parent cell line from which the xenograft was prepared. Moderate complexity tissue microarrays constructed from murine xenografts are excellent validation tools for initial assessment of interphase FISH probe specificity.