Web-based tissue microarray image data analysis: initial validation testing through prostate cancer Gleason grading

Web-grading-a tool to test personal grading of renal and prostate cancer

Only a few pathologists have the opportunity to verify their personal grading through objective assessment. This study introduces a web-based grading platform to facilitate and validate the grading of renal cell carcinoma and prostate cancer. Two representative images of two clinically annotated cohorts of 100 cases each of prostate and renal cell carcinoma were used. Each participant was asked to grade a tumor series utilizing a three tiered grading system. Finally, a Kaplan-Meier curve was drawn, and the log-rank test was used for statistical testing of the p-value. The grading of 22 participants (68%) achieved prognostic significance. Further analysis highlighted that only two pathologists were able to reliably separate low- and high-grade tumors from intermediate grades. The limitations of this study are the low number of participants in each of the cohorts and the potential selection bias of the tumor images. This web-based grading portal facilitates the assessment of the validity of grading by individual pathologists. The observation that most participants can only successfully identify high- or low-grade tumors but cannot discriminate between more subtle intermediate grades does indicate that there is a need for the development of more formal training programs for tumor grading.

Guidelines and considerations for conducting experiments using tissue microarrays

Tissue microarrays (TMAs) represent a powerful method for undertaking large-scale tissue-based biomarker studies. While TMAs offer several advantages, there are a number of issues specific to their use which need to be considered when employing this method. Given the investment in TMA-based research, guidance on design and execution of experiments will be of benefit and should help researchers new to TMA-based studies to avoid known pitfalls. Furthermore, a consensus on quality standards for TMA-based experiments should improve the robustness and reproducibility of studies, thereby increasing the likelihood of identifying clinically useful biomarkers. In order to address these issues, the National Cancer Research Institute Biomarker and Imaging Clinical Studies Group organized a 1-day TMA workshop held in Nottingham in May 2012. The document herein summarizes the conclusions from the workshop. It includes guidance and considerations on all aspects of TMA-based research, including the pre-analytical stages of experimental design, the analytical stages of data acquisition, and the postanalytical stages of data analysis. A checklist is presented which can be used both for planning a TMA experiment and interpreting the results of such an experiment. For studies of cancer biomarkers, this checklist could be used as a supplement to the REMARK guidelines.

Gleason grading of prostate cancer in needle core biopsies: a comparison of general and urologic pathologists

BACKGROUND AND OBJECTIVES

The Gleason grading of prostate carcinoma (PCa) in needle core biopsies is a major determinant used in management planning. The objective of this study was to evaluate the concordance between general pathologists Gleason grading and that of a urologic pathologist in our community.

DESIGN AND SETTING

Retrospective review conducted at three tertiary care hospitals in Jeddah and Riyadh for all prostatic biopsies with carcinoma from January 2002 to January 2011.

METHODS

Gleason scores assigned by the original pathologist were compared with that of the reviewing urologic pathologists. Biopsies were originally obtained and diagnosed at different referring hospitals and independent laboratories. The kappa test was used to evaluate agreement between the original and review scores.

RESULTS

For 212 biopsies the exact concordance of the Gleason score assigned by the original pathologist and the reviewer was 38.7% (82/212). However, when grouped into the main four-score categories of 2-4, 5-6, 7, and 8 or greater, disagreement was noted in 88 (41.5%) biopsies; 87 were upgraded and 1 was downgraded on review. When grouped into two-score categories of low grade (≤6) and high grade (≥7), disagreement was noted in 32 (15%) of the biopsies.

CONCLUSION

Gleason grade score shows that there was only slight to fair agreement between outside and review scoring (kappa=0.43). When using only low versus high grade categorization, there was good agreement (kappa=0.69). Almost all of the cases with score disagreement were upgraded on review.

Datamining approach for automation of diagnosis of breast cancer in immunohistochemically stained tissue microarray images

Cancer of the breast is the second most common human neoplasm, accounting for approximately one quarter of all cancers in females after cervical carcinoma. Estrogen receptor (ER), Progesteron receptor and human epidermal growth factor receptor (HER-2/neu) expressions play an important role in diagnosis and prognosis of breast carcinoma. Tissue microarray (TMA) technique is a high throughput technique which provides a standardized set of images which are uniformly stained, facilitating effective automation of the evaluation of the specimen images. TMA technique is widely used to evaluate hormone expression for diagnosis of breast cancer. If one considers the time taken for each of the steps in the tissue microarray process workflow, it can be observed that the maximum amount of time is taken by the analysis step. Hence, automated analysis will significantly reduce the overall time required to complete the study. Many tools are available for automated digital acquisition of images of the spots from the microarray slide. Each of these images needs to be evaluated by a pathologist to assign a score based on the staining intensity to represent the hormone expression, to classify them into negative or positive cases. Our work aims to develop a system for automated evaluation of sets of images generated through tissue microarray technique, representing the ER expression images and HER-2/neu expression images. Our study is based on the Tissue Microarray Database portal of Stanford university at http://tma.stanford.edu/cgi-bin/cx?n=her1, which has made huge number of images available to researchers. We used 171 images corresponding to ER expression and 214 images corresponding to HER-2/neu expression of breast carcinoma. Out of the 171 images corresponding to ER expression, 104 were negative and 67 were representing positive cases. Out of the 214 images corresponding to HER-2/neu expression, 112 were negative and 102 were representing positive cases. Our method has 92.31% sensitivity and 93.18% specificity for ER expression image classification and 96.67% sensitivity and 88.24% specificity for HER-2/neu expression image classification.

A Decade of Tissue Microarrays: Progress in the Discovery and Validation of Cancer Biomarkers

This year, 2008, marks the 10-year anniversary of the development of the modern tissue microarray (TMA). During the last decade, the use of TMAs has grown steadily and accounts for a small but increasing percentage of all cancer biomarker studies performed. The growing popularity of TMA-based studies attests to their benefits in the discovery and validation of new biomarkers. This review will focus on these benefits, but also on the faults of TMAs and the challenges of TMA studies that have been overcome in the last decade. We will also discuss the role of TMAs in the latest revolution in cancer treatment, the use of targeted drug therapy.

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guidelines for gene expression localization experiments: the minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). MISFISHIE is modeled after the Minimum Information About a Microarray Experiment (MIAME) specification for microarray experiments. Both guidelines define what information should be reported without dictating a format for encoding that information. MISFISHIE describes six types of information to be provided for each experiment: experimental design, biomaterials and treatments, reporters, staining, imaging data and image characterizations. This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.

Interobserver reproducibility of Gleason grading: evaluation using prostate cancer tissue microarrays

OBJECTIVES

Due to PSA screening and increased awareness, prostate cancer (PCa) is identified earlier resulting in smaller diagnostic samples on prostate needle biopsy. Because Gleason grading plays a critical role in treatment planning, we undertook a controlled study to evaluate interobserver variability among German pathologists to grade small PCas using a series of tissue microarray (TMA) images.

METHODS

We have previously demonstrated excellent agreement in Gleason grading using TMAs among expert genitourinary pathologists. In the current study, we identified 331 TMA images (95% PCa and 5% benign) to be evaluated by an expert PCa pathologist and subsequently by practicing pathologists throughout Germany. The images were presented using the Bacus Webslide Browser on a CD-ROM. Evaluations were kept anonymous and participant's scoring was compared to the expert's results.

RESULTS

A total of 29 German pathologists analysed an average of 278 images. Mean percentage of TMA images which had been assigned the same Gleason score (GS) as done by the expert was 45.7%. GSs differed by no more than one point (+/-1) in 83.5% of the TMA samples evaluated. The respondents were able to correctly assign a GS into clinically relevant categories (i.e. <7, 7, >7) in 68.3% of cases. A total of 75.9% respondents under-graded the TMA images. Gleason grading agreement with the expert reviewer correlated with the number of biopsies evaluated by the pathologist per week. Years of diagnostic experience, self-description as a urologic pathologist or affiliation with a university hospital did not correlate with the pathologist's performance.

CONCLUSION

The vast majority of participants under-graded the small tumors. Clinically relevant GS categories were correctly assigned in 68% of cases. This raises a potentially significant problem for pathologists, who have not had as much experience evaluating small PCas.

Assessing expression of apoptotic markers using large cohort tissue microarrays

Apoptotic markers include proteins from the intrinsic and extrinsic pathways. These cascades include both pro-apoptotic and anti-apoptotic elements. The expression levels of these elements can be assessed by immunohistochemistry (IHC) and can indicate general trends in prov-ersus anti-apoptotic tendencies of the cells. IHC is particularly useful when studying large cohorts of paraffin-embedded specimens. Advances in tissue microarray (TMA) technology have facilitated evaluation of large cohorts of specimens, as cores from hundreds of patients can be represented on a single glass slide and stained in a uniform fashion. In this chapter, we discuss construction and staining methods of TMAs and present examples of assessment of apoptotic marker expression in malignant and benign cells using a novel method of automated, quantitative analysis of in situ protein expression.

Reproducibility and reliability of tumor grading in urological neoplasms

Histopathologic tumor grading reflects the degree of differentiation of a given tumor and for most urological tumors grading is an important factor in predicting their biological aggressiveness. Consequently, the clinical management of tumor patients is often strongly influenced by the tumor grade, provided by pathologists. This implicates that an ideal grading system should not only be of high prognostic relevance, but also of high reproducibility among different pathologists. To this end individual histological grading systems have been developed for different tumor entities and even for a given tumor type several grading systems have been proposed. All of these grading systems possess an inherent degree of subjectivity and consequently, both intra- and interobserver variability exist. In this review, grading systems for the most frequent urological tumors (i.e. prostate cancer, renal cell carcinoma, and urothelial tumors) are mentioned and data on the reproducibility and reliability of the most commonly used grading systems are summarized.

Clinical validation of breast cancer biomarkers using tissue microarray technology

The results of previous studies done in our laboratory on breast cancer gene expression profile, using DNA microarrays, led to the discovery of several genes associated with breast cancer progression. Further evaluation of these genes and their involvement at various stages of cancer progression required performance of immunohistochemistry on thousands of different tissue blocks. Tissue microarray (TMA) technology facilitates rapid translation of DNA microarrays results to clinical specimens by using immunohistochemical analysis of protein expression. DNA microarray analysis done in our laboratory showed a significantly higher expression of prostatic-specific antigen (PSA) in invasive ductal carcinomas as compared to ductal carcinoma in situ, a finding contrary to the previously published data for PSA immunoreactivity in breast carcinomas. To find out whether TMA strategy could be used to explore the expression of the candidate genes involved in the breast cancer progression, we constructed a breast cancer progression TMA. It consisted of 2 normal ductal epithelium, 8 ductal carcinoma in situ, 19 invasive ductal carcinomas, and 3 metastatic ductal carcinomas of breast in triplets. Two prostatic adenocarcinomas and 2 normal colons were used as positive and negative controls, respectively. We first used well-documented and well-tested markers, such as antibodies to estrogen receptor, progesterone receptor, and p53. Results of these 3 antibodies were according to the previously published data. To validate our result, we then used antibody to PSA and looked for the expression of this protein on breast cancer progression TMA. Except for the 2 positive controls all 98 cores were found to be negative for PSA expression highlighting the importance of validation studies for DNA microarray results.

Morphological features of TMPRSS2-ERG gene fusion prostate cancer

The TMPRSS2-ETS fusion prostate cancers comprise 50-70% of the prostate-specific antigen (PSA)-screened hospital-based prostate cancers examined to date, making it perhaps the most common genetic rearrangement in human cancer. The most common variant involves androgen-regulated TMPRSS2 and ERG, both located on chromosome 21. Emerging data from our group and others suggests that TMPRSS2-ERG fusion prostate cancer is associated with higher tumour stage and prostate cancer-specific death. The goal of this study was to determine if this common somatic alteration is associated with a morphological phenotype. We assessed 253 prostate cancer cases for TMPRSS2-ERG fusion status using an ERG break-apart FISH assay. Blinded to gene fusion status, two reviewers assessed each tumour for presence or absence of eight morphological features. Statistical analysis was performed to look for significant associations between morphological features and TMPRSS2-ERG fusion status. Five morphological features were associated with TMPRSS2-ERG fusion prostate cancer: blue-tinged mucin, cribriform growth pattern, macronucleoli, intraductal tumour spread, and signet-ring cell features, all with p-values < 0.05. Only 24% (n=30/125) of tumours without any of these features displayed the TMPRSS2-ERG fusion. By comparison, 55% (n=38/69) of cases with one feature (RR=3.88), 86% (n=38/44) of cases with two features (RR=20.06), and 93% (n=14/15) of cases with three or more features (RR=44.33) were fusion positive (p<0.001). To our knowledge, this is the first study that demonstrates a significant link between a molecular alteration in prostate cancer and distinct phenotypic features. The strength of these findings is similar to microsatellite unstable colon cancer and breast cancer involving BRCA1 and BRCA2 mutations. The biological effect of TMPRSS2-ERG overexpression may drive pathways that favour these common morphological features that pathologists observe daily. These features may also be helpful in diagnosing TMPRSS2-ERG fusion prostate cancer, which may have both prognostic and therapeutic implications.

TAMEE: data management and analysis for tissue microarrays

Background

With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories.

Results

TAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator.

Conclusion

We have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from .

Prostate cancer metastasis: role of the host microenvironment in promoting epithelial to mesenchymal transition and increased bone and adrenal gland metastasis

BACKGROUND

The ARCaP cell line was established from the ascites fluid of a patient with metastatic prostate cancer. This study characterized the host microenvironmental role in cancer progression, epithelial to mesenchymal transition (EMT), and bone and adrenal metastasis in parental ARCaP and its derived cell subclones.

METHODS

Cytogenetic profiles, growth, migration, invasion, cellular interaction, drug sensitivities, and gene expression of ARCaP cell subclones were compared. In vivo gene expression, behavior, and metastasis of ARCaP subclones were analyzed by serial intracardiac injections into SCID mice.

RESULTS

ARCaP(E) cells, with cobblestone morphology, underwent EMT through cellular interaction with host bone and adrenal gland. Lineage-derived ARCaP(M) cells, with spindle-shape fibroblastic morphology, exhibited decreased cell adhesion and increased metastasis to bone and adrenal gland. Cytogenetic analyses of parental and ARCaP subclones confirmed their clonality.

CONCLUSIONS

ARCaP uniquely models the molecular basis of prostate cancer bone and adrenal metastases and epithelial to mesenchymal transition.

Tissue microarrays: applications in urological cancer research

Tissue microarrays (TMAs) are used to simultaneously study the expression of proteins in hundreds of tissue samples, offering the important advantage to screen large tissue banks for biomarker expression and to simultaneously examine serial sections obtained from the same tumor specimen by a time- and cost-effective analytical approach. This review article presents an overview of the importance and the impact of this technique in cancer research with increasing number of investigations using TMAs in its eighth anniversary. Its application, limitations, and selected previous study results regarding urologic malignancies are presented and discussed.

Tissue microarrays: bridging the gap between research and the clinic

Tissue microarrays are a high-throughput method for the investigation of biomarkers in multiple tissue specimens at once. This technique allows for the analysis of up to 500 tissue samples in a single experiment using immunohistochemistry and in situ hybridization. Recently, cell lines and xenografts have been reduced to a tissue microarray format and are being applied to preclinical drug development. In clinical research, tissue microarrays are applied at multiple levels: comprehensive analysis of samples in the context of a clinical trial or across a population. Tissue microarrays play a central role in translational research, facilitating the discovery of molecules that have potential roles in the diagnosis, prognosis and prediction of response to therapy.

The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line

Background

The Tissue Microarray (TMA) facilitates high-throughput analysis of hundreds of tissue specimens simultaneously. However, bottlenecks in the storage and manipulation of the data generated from TMA reviews have become apparent. A number of software applications have been developed to assist in image and data management; however no solution currently facilitates the easy online review, scoring and subsequent storage of images and data associated with TMA experimentation.

Results

This paper describes the design, development and validation of the Virtual Tissue Matrix (VTM). Through an intuitive HTML driven user interface, the VTM provides digital/virtual slide based images of each TMA core and a means to record observations on each TMA spot. Data generated from a TMA review is stored in an associated relational database, which facilitates the use of flexible scoring forms. The system allows multiple users to record their interpretation of each TMA spot for any parameters assessed. Images generated for the VTM were captured using a standard background lighting intensity and corrective algorithms were applied to each image to eliminate any background lighting hue inconsistencies or vignetting.

Validation of the VTM involved examination of inter-and intra-observer variability between microscope and digital TMA reviews. Six bladder TMAs were immunohistochemically stained for E-Cadherin, β-Catenin and PhosphoMet and were assessed by two reviewers for the amount of core and tumour present, the amount and intensity of membrane, cytoplasmic and nuclear staining.

Conclusion

Results show that digital VTM images are representative of the original tissue viewed with a microscope. There were equivalent levels of inter-and intra-observer agreement for five out of the eight parameters assessed. Results also suggest that digital reviews may correct potential problems experienced when reviewing TMAs using a microscope, for example, removal of background lighting variance and tint, and potential disorientation of the reviewer, which may have resulted in the discrepancies evident in the remaining three parameters.

Tissue microarrays: applications in neuropathology research, diagnosis, and education

Tissue microarrays (TMAs) are composite paraffin blocks constructed by extracting cylindrical tissue core "biopsies" from different paraffin donor blocks and re-embedding these into a single recipient (microarray) block at defined array coordinates. Using this technique, up to 1000 or more tissue samples can be composited into a single paraffin block. Tissue microarrays permit high-volume simultaneous analysis of molecular targets at the DNA, mRNA, and protein levels under identical, standardized conditions on a single glass slide, and also provide maximal preservation and utilization of limited and irreplaceable archival tissue samples. This versatile technique facilitates retrospective and prospective human tissue studies, animal tissue studies, and cell line cytospin cell block studies. In this review, we present the technical aspects of TMA construction and sectioning, validation aspects of the technique, TMA advantages and limitations, and a sampling of the broad range of TMA uses in modern neuropathologic clinical diagnosis, research, and education. A specific illustration of the most widely employed and increasingly important TMA application is also presented: confirmation via TMA-based immunohistochemistry of the differential expression of a marker (IGFBP2) initially identified by gene expression profiling to be overexpressed in glioblastoma.

Tissue microarrays and their relevance to the urologist

PURPOSE

We review important aspects of TMA methodology and discuss its wide range of clinical applications with particular emphasis on key clinical studies. We also provide an update on recent and projected uses of this technology to help the urologist improve care in oncology patients.

MATERIALS AND METHODS

A directed MEDLINE literature review of TMAs was performed. Important publications that have shaped our understanding of TMAs were selected for review. They were augmented by manual searches and our personal bibliographic collections.

RESULTS

The TMA is a high throughput molecular biology technique that can significantly accelerate the processing of a large number of tissue specimens with excellent quality, good reliability and the preservation of original tissue. TMA studies demonstrate their accuracy and reliability compared to those of standard histological techniques and correlate with clinicopathological information to determine disease progression and prediction of the clinical outcome.

CONCLUSIONS

This review represents an overview and update for the urologist on TMAs and their clinical applications in urological oncology. In the future it is anticipated that the outcomes of this method will be used to assist in the diagnosis, prognosis and development of novel therapies in individual patients.

Advances in cancer tissue microarray technology: Towards improved understanding and diagnostics

Over the past few years, tissue microarray (TMA) technology has been established as a standard method for assessing the expression of proteins or genes across large sets of tissue specimens. It is being adopted increasingly among leading research institutions around the world and utilized in cancer research in parallel with the cDNA microarray technology. This article summarizes various aspects of cancer understanding and diagnostics in which TMA has had great impact. Although tremendous advances continue to be made to facilitate imaging and archiving of TMA specimens, automatic evaluation and quantitative analysis of TMA still remains an important challenge for modern investigators.

Internet-based Profiler system as integrative framework to support translational research

Background

Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis and prognosis by integrating tissue microarray (TMA) technology and an internet-database tool, Profiler. TMA technology allows investigators to study hundreds of patient samples on a single glass slide resulting in the conservation of tissue and the reduction in inter-experimental variability. The Profiler system allows investigator to reliably track, store, and evaluate TMA experiments. Here within we describe the process that has evolved through an empirical basis over the past 5 years at two academic institutions.

Results

The generic design of this system makes it compatible with multiple organ system (e.g., prostate, breast, lung, renal, and hematopoietic system,). Studies and folders are restricted to authorized users as required. Over the past 5 years, investigators at 2 academic institutions have scanned 656 TMA experiments and collected 63,311 digital images of these tissue samples. 68 pathologists from 12 major user groups have accessed the system. Two groups directly link clinical data from over 500 patients for immediate access and the remaining groups choose to maintain clinical and pathology data on separate systems. Profiler currently has 170 K data points such as staining intensity, tumor grade, and nuclear size. Due to the relational database structure, analysis can be easily performed on single or multiple TMA experimental results. The TMA module of Profiler can maintain images acquired from multiple systems.

Conclusion

We have developed a robust process to develop molecular biomarkers using TMA technology and an internet-based database system to track all steps of this process. This system is extendable to other types of molecular data as separate modules and is freely available to academic institutions for licensing.

Comparison of monoclonal antibody (P504S) and polyclonal antibody to alpha methylacyl-CoA racemase (AMACR) in the work-up of prostate cancer

AIM

Studies using a monoclonal (P504S) and a polyclonal antibody (p-AMACR) to alpha-methylacyl-CoA racemase (AMACR) have shown variable expression in prostate cancer (PCa). The goal is to compare the sensitivity of both antibodies in PCa and evaluate their utility in the work-up of atypical prostate needle biopsies (NBXs).

METHODS AND RESULTS

A tissue microarray (TMA) with 248 samples of benign prostate, high-grade prostatic intraepithelial neoplasia (HGPIN) and PCa samples, 20 NBXs with minute PCa and 32 NBXs with 'atypical' foci were stained with P504S and p-AMACR. Ninety percent of PCa (76/76 TMA, 16/20 NBXs) showed predominantly strong p-AMACR expression while 87% (65/69 TMA, 16/20 NBXs) showed variable P504S expression (sensitivity 90% versus 87%, P = 0.10). In HGPIN, P504S and p-AMACR were positive in 77% and 91% of samples, respectively. In the 'atypical' NBXs group, 53% were classified as PCa, 12% benign and 35% atypical, suspicious for PCa, after review of the basal marker. Of atypical, suspicious for PCa, P504S/p-AMACR helped convert the diagnosis to PCa in 5/11 (45%) cases, where, despite negative basal cell markers, morphology was less than optimal.

CONCLUSIONS

Differences between P504S and p-AMACR appear marginal and clinically insignificant. AMACR is negative in a subset of unequivocal minute PCa with both antibodies. However, when utilized in proper context, AMACR may offer significant advantage in converting an 'atypical' diagnosis to PCa where morphology and basal markers are less than optimal in resolving the diagnosis.

Tissue microarrays – automated analysis and future directions

Tissue microarrays have rapidly become a vital tool in the analysis of protein biomarkers on large patient cohorts. Composed of hundreds of miniature histologic tissue cores taken from patient tumors and arrayed in a grid pattern, tissue microarrays have great potential for automation. However, unlike DNA/RNA expression arrays, they contain spatial information, such that successful automation requires both the ability to quantitateandlocalize biomarkers within the tissue. This review traces tissue microarray analysis from the simplest of systems (visual inspection) to dedicated, automated quantitative analyzers capable of localizing biomarkers to sub-cellular compartments. It focuses on the importance of automating the process of tissue microarray analysis, while commenting on the inherent problems associated with both manual and automated analysis. Finally, it discusses the future of automated tissue microarray analysis, emphasizing the many areas of development and potential improvement.

An automated procedure to properly handle digital images in large scale tissue microarray experiments

Tissue Microarray (TMA) methodology has been recently developed to enable "genome-scale" molecular pathology studies. To enable high-throughput screening of TMAs automation is mandatory, both to speed up the process and to improve data quality. In particular, in acquiring digital images of single tissues (core sections) a crucial step is the correct recognition of each tissue position in the array. In fact, further reliable data analysis is based on the exact assignment of each tissue to the corresponding tumor. As most of the times tissue alignment in the microarray grid is far from being perfect, simple strategies to perform proper acquisition do not fit well. The present paper describes a new solution to automatically perform grid location assignment. We developed an ad hoc image processing procedure and a robust algorithm for object recognition. Algorithm accuracy tests and assessment of working constraints are discussed. Our approach speeds up TMA data collection and enables large scale investigation.

Tissue microarrays: applications in genomic research

The widespread application of tissue microarrays in cancer research and the clinical pathology laboratory demonstrates a versatile and portable technology. The rapid integration of tissue microarrays into biomarker discovery and validation processes reflects the forward thinking of researchers who have pioneered the high-density tissue microarray. The precise arrangement of hundreds of archival clinical tissue samples into a composite tissue microarray block is now a proven method for the efficient and standardized analysis of molecular markers. With applications in cancer research, tissue microarrays are a valuable tool in validating candidate markers discovered in highly sensitive genome-wide microarray experiments. With applications in clinical pathology, tissue microarrays are used widely in immunohistochemistry quality control and quality assurance. The timeline of a biomarker implicated in prostate neoplasia, which was identified by complementary DNA expression profiling, validated by tissue microarrays and is now used as a prognostic immunohistochemistry marker, is reviewed. The tissue microarray format provides opportunities for digital imaging acquisition, image processing and database integration. Advances in digital imaging help to alleviate previous bottlenecks in the research pipeline, permit computer image scoring and convey telepathology opportunities for remote image analysis. The tissue microarray industry now includes public and private sectors with varying degrees of research utility and offers a range of potential tissue microarray applications in basic research, prognostic oncology and drug discovery.

Trefoil factor 3 overexpression in prostatic carcinoma: prognostic importance using tissue microarrays

BACKGROUND

Human intestinal trefoil factor 3 (TFF3) is a member of a family of polypeptides encoded by a cluster of genes on chromosome 21. Through gene expression profiling studies TFF3 mRNA has been found to be overexpressed in prostate cancer.

METHODS

We used immunochemistry on tissue microarrays and software tools, collectively referred to as TMAJ, for online assessment of staining to analyze samples from 294 primary tumors and 61 metastatic lesions.

RESULTS

Applying a cutoff of 20% of cells staining as positive, the frequency of staining was 18.8% in normal (51 of 272) and 47.0% in primary tumors (126 of 268), P < 0.0001, Wilcoxon rank sum). Expression of TFF3 in metastatic prostate cancer was similar to that in primary tumors. TFF3 expression was not associated with time to biochemical recurrence, development of distant metastasis, or death due to prostate cancer. Scoring data derived from visual estimation of expression correlated highly with semi-automated image analysis using the Automated Cellular Imaging System (ACIS) from Chromavision, Inc.

CONCLUSIONS

These studies validate that TFF3 is overexpressed at the protein level in a subset of primary and metastatic prostate cancers, show the first use of the TMAJ database, and demonstrate the ability to semi-automatically scan and score immunohistochemically stained tissue microarray slides.

Tissue microarrays

The identification of disease-related genes is a major focus of modern biomedical research. Recent techniques, including array-based platforms for molecular profiling of disease tissues such as DNA arrays for expression profiling or matrix comparative genomic hybridization, allow for the comprehensive screening of the whole genome in a single experiment. Consequently, thousands of candidate genes have already been identified that may be linked to disease development and progression, and the process of lead discovery continues unimpeded. The evaluation of the clinical value of such leads is challenging because thousands of well-characterized tissue specimens must be analyzed. Tissue microarray (TMA) technology enables high-throughput tissue analyses to keep pace with the rapid process of lead discovery. With this technique, up to 1000 minute tissue samples are brought into an array format and analyzed simultaneously. The TMA technology is a fast, cost-effective, and statistically powerful method that will substantially facilitate translational research.

Tissue microarrays: a current medical research tool

Recent research in molecular biology has identified a significant number of novel markers, which may have diagnostic, prognostic and therapeutic significance. This is particularly pertinent in the field of cancer. Validation of these markers in multiple clinical specimens is currently performed by traditional histopathological techniques, which are disappointingly time consuming, labour intensive and, therefore, economically costly. These limitations have hampered the introduction of many novel markers into everyday clinical practice. The tissue microarray (TMA) is a high throughput technique, which allows the rapid and cost effective validation of novel markers in multiple pathological tissue specimens. Tissue from up to a 1000 histology blocks can be arrayed accurately onto a newly created paraffin block, at designated locations. Subsequently, morphological and molecular investigations can be performed to determine the clinical significance of the novel markers tested. It is now firmly established that the TMA can significantly accelerate the processing of a very large number of tissue specimens with excellent quality, good reliability and preservation of original tissue, with ultimate clinical benefit.

Rapid and large-scale transition of new tumor biomarkers to clinical biopsy material by innovative tissue microarray systems

A rapidly increasing number of studies are being published providing significant results by the use of tissue microarrays (TMAs), ie, paraffin blocks composed of multiple specimens. The numerous advantages of this technology are obvious and have thus stimulated many constructors to evolve and improve different technical approaches. With TMAs, multiple specimens can be simultaneously investigated with different in situ techniques under identical laboratory conditions, resulting in a dramatic time and cost reduction compared with conventional pathologic studies. Furthermore, this technology is less exhausting for the finite original donor material, allowing for a significantly increased number of assays per each case. Against the background of decoding the human genome and the widespread application of high-density cDNA microarrays, the next challenge will be to apply the genome discoveries to the clinical setting. For pathologists, TMAs represent an ideal adjunct and can be very useful for the rapid and high-throughput discovery and validation of countless candidate biomarkers, assessing their prognostic and predictive value and identifying further therapy targets. This article provides a review of different TMA technologies and addresses the technical aspects of their construction and their validity in different applications through data from the literature along with the authors' own experiences.

Markers for the development of early prostate cancer

Biochemical and genetic changes precede histologically identifiable changes accompanying cell transformation often by months or years. De-expression of the extracellular matrix adhesive glycoprotein tenascin and the cell-to-cell adherent protein E-cadherin have been suggested as markers of early neoplastic change in prostate epithelial cells. Previous studies have been inconclusive, probably due to epitope masking. This study examined 2,378 biopsy cores from 289 prostates using a heat antigen retrieval protocol at low pH to improve the accuracy of detection. Tenascin and E-cadherin de-expression was correlated with purinergic receptor and telomerase-associated protein labelling, as well as prostate-specific antigen (PSA) levels and Gleason scores. E-cadherin was a poor marker, as it was expressed in all lesions except carcinomas of the highest Gleason score. Tenascin was maximally expressed in the extracellular matrix and acinar basement membrane in normal and prostatic intraepithelial neoplasia tissue. In prostate cancer tissue, tenascin expression did not correlate with Gleason score but was significantly de-expressed as purinergic receptor and telomerase-associated protein expression increased. Marked changes in tenascin, telomerase-associated protein, and purinergic receptor expression were apparent before any histological abnormalities were visible by haematoxylin and eosin (H&E) stain, making these potential markers for early and developing prostate cancer. Moreover, the potential increased accuracy of diagnosis of underlying prostate cancer using purinergic receptor translocation (PRT) assessment suggests that PSA levels may be more accurate than has generally been supposed when apparent false negatives arising from H&E-based diagnoses are correctly categorized.

The polycomb group protein EZH2 is involved in progression of prostate cancer

Prostate cancer is a leading cause of cancer-related death in males and is second only to lung cancer. Although effective surgical and radiation treatments exist for clinically localized prostate cancer, metastatic prostate cancer remains essentially incurable. Here we show, through gene expression profiling, that the polycomb group protein enhancer of zeste homolog 2 (EZH2) is overexpressed in hormone-refractory, metastatic prostate cancer. Small interfering RNA (siRNA) duplexes targeted against EZH2 reduce the amounts of EZH2 protein present in prostate cells and also inhibit cell proliferation in vitro. Ectopic expression of EZH2 in prostate cells induces transcriptional repression of a specific cohort of genes. Gene silencing mediated by EZH2 requires the SET domain and is attenuated by inhibiting histone deacetylase activity. Amounts of both EZH2 messenger RNA and EZH2 protein are increased in metastatic prostate cancer; in addition, clinically localized prostate cancers that express higher concentrations of EZH2 show a poorer prognosis. Thus, dysregulated expression of EZH2 may be involved in the progression of prostate cancer, as well as being a marker that distinguishes indolent prostate cancer from those at risk of lethal progression.

Inadequate formalin fixation decreases reliability of p27 immunohistochemical staining: probing optimal fixation time using high-density tissue microarrays

Immunohistochemical analysis of molecular targets in clinical tissues is increasingly becoming central to our ability to render diagnoses, to predict prognosis, to select patients for appropriate therapies, and to provide surrogate end points for therapeutic monitoring. For example, reduction of immunohistochemical staining for the cyclin-dependent kinase inhibitor p27(Kip1) has been proposed as a potential prognostic biomarker in prostate, breast, and gastrointestinal tumors. We observed that with our standard formalin fixation in rapidly processed (same-day) radical prostatectomy specimens, there is often a gradient of p27(Kip1) staining in normal prostate epithelium, with more staining near the periphery and less staining toward the center of the sample. This raised the hypothesis that the reliability of staining for p27(Kip1) is decreased in inadequately fixed tissues. The implications of this, if true, are that many studies using p27(Kip1) for prognostic purposes may be subject to unpredictable artifacts, and hence unreliable results, if the fixation of the specimens is not well controlled. The objectives of the present study were (1) to formally test the hypothesis that inadequate fixation time is responsible for apparent loss of p27(Kip1) nuclear staining and (2) to test a recently proposed method for improving the uniformity of immmunohistochemical staining using formalin injection. Prostate tissue sections from radical prostatectomy specimens were either processed immediately (zero time fixation) or fixed for 1, 2, 3, or 8 days in 10% neutral buffered formalin before processing into paraffin. To assure identical antigen retrieval and immunohistochemical staining conditions for specimens fixed for different lengths of time, 2 high-density tissue microarrays (TMAs), containing 564 tissue samples (0.6 mm in diameter) were constructed. Based on an estimate of the percentage of nuclei in normal prostatic epithelial secretory cells with strong staining, quality of p27(Kip1) staining was graded in a blinded fashion with respect to fixation time. There was a significant increase in the percentage of cores that were scored as "strong" as fixation time increased from 0 (same-day processing) to 1 or more days (P <.0001). Interestingly, even at 8 days of fixation, there was excellent staining that was superior to the same-day processing. Based on these results, we conclude the following: (1) for large clinical specimens that have been fixed briefly to decrease diagnostic turn-around time, the reliability of interpretation of immunohistochemical staining may be quite limited; (2) for p27(Kip1), decreased antigen staining as a result of the widely held concept of "overfixation" is much less of a problem than "underfixation"; (3) formalin injection produces a marked improvement in staining for several markers, including p27(Kip1); and (4) high-density TMAs, which assure identical test conditions, provide an excellent platform on which to evaluate the effects of tissue fixation on immunohistochemical staining.

Molecular markers and determinants of prostate cancer metastasis

Although intensely studied, the molecular and biochemical determinants of prostate cancer development and progression remain ill-defined. Moreover, current markers and methodologies cannot distinguish between a tumor that will remain indolent and not impinge on patient survival, versus a tumor with aggressive traits culminating in metastatic spread and death. Once prostate cancer is confirmed the most significant threat to a patient's survival and quality of life involves tumor metastasis. Radical surgery notwithstanding, prostate cancer accounts for 10% of all cancer-related deaths primarily arising through development of metastasis. Metastasis markers demonstrating an acceptable level of reliability are an obvious necessity if disproportionate and costly treatment is to be avoided and a reasonably accurate determination of clinical prognosis and measure of successful response to treatment is to be made. Therapeutic strategies that specifically inhibit metastatic spread are not presently possible and may not become available in the immediate future. This is because, while localized tumorigenesis has been relatively amenable to detection, analysis and treatment, metastasis remains a relatively undefined, complex and underexplored area of prostate cancer research. New findings in the field such subclasses of genes called metastasis suppressors and cancer progression suppressors, have opened up exciting avenues of investigation. We review current methodological approaches, model experimental systems and genes presently known or having potential involvement in human prostate cancer metastasis.

Relational database structure to manage high-density tissue microarray data and images for pathology studies focusing on clinical outcome: the prostate specialized program of research excellence model

With the completion of the Human Genome Project and high-throughput screening methods using cDNA array and tissue microarray (TMA) technology, there is a pressing need to manage the voluminous data sets generated from these types of investigations. Herein is described a database model to handle 1) clinical and pathology data, 2) TMA location information, and 3) web-based histology results. The model is useful for managing clinical, pathology, and molecular data on >1300 prostate cancer patients dating back to 1995 from the University of Michigan Specialized Program of Research Excellence for prostate cancer. The key components in this multidatabase model are 1) the TMA database, 2) the TMA-image database (TMA-I DB), and 3) the prostate pathology and clinical information databases. All databases were created in Microsoft Access (Microsoft, Redmond, WA). Desired patient, tissue, block, diagnosis, array location, and respective clinical and pathology information is obtained by linking the unique identifier fields among database tables. The TMA database is comprised of interrelated data from 336 prostate cancer patients transferred into 19 TMA blocks with 5451 TMA biopsy cores. Tissue samples include 1695 normal prostate, 3171 prostate cancer, 464 prostatic intraepithelial neoplasia, and 121 atrophy. All 19 TMA blocks have been analyzed over the Internet for several immunohistochemical biomarkers including E-cadherin, prostate-specific antigen, p27(Kip1), and Ki-67 labeling index. This system facilitates the statistical analysis of high-density TMA data with clinical and pathology information in an efficient and cost-effective manner. Because the review is performed over the Internet, this system is ideal for collaborative multi-institutional studies.