Tissue microarray (TMA) technology: miniaturized pathology archives for high-throughput in situ studies

High-throughput molecular pathology in human tissues as a method for driving drug discovery

To facilitate prioritization of potential drug targets, gene expression can be localized to individual cell types in normal and diseased tissues. Given the complexity of molecular physiology and pathology, the creation of large-scale molecular pathology databases collating data obtained from human tissues is a challenging marriage of old and new technologies, particularly when considering the many issues that preclude easy access to substantial quantities of human tissues. Molecular pathology databases are powerful tools and are essential for early-stage drug discovery, enabling informed decisions to be made with respect to scientific direction and follow-up research.

In Situ Hybridization: An Informative Technique for Pigment Cell Researchers

Many cellular events are regulated at the transcriptional level. Recent technical advances such as DNA microarray have made it possible to determine mRNA profiles of cultured cells or tissues. However, since it is still impossible to completely simulate the in vivo environment in culture conditions, mRNA profiles of cultured cells are not perfect representatives of original cells. Furthermore, for cells that exist at lower densities, mRNA profiling using tissue samples would be difficult. By using tissue in situ hybridization, mRNA levels of genes in tissues can be determined at cellular resolution. Although throughput of tissue in situ hybridization is not high enough for mRNA profiling, it may be sufficient to investigate temporal/spatial expression profiles of genes that are known to be important or found to be interesting in high-throughput transcriptome/proteome analyses. Recent technical advances have made it easier for everybody to perform tissue in situ hybridization using normal experimental instruments with sufficient sensitivity to detect most genes. Although this technique has been utilized mainly in developmental biology, it will be fully advantageous when combined with high-throughput comprehensive transcriptome/proteome analyses.

Differential gene expression of Eph receptors and ephrins in benign human tissues and cancers

BACKGROUND

Eph receptors and their ligands, the ephrins, represent a large class of cell-cell communication molecules with well-defined developmental functions. Their role in healthy adult tissues and in human disease is still largely unknown, although diverse roles in carcinogenesis have been postulated.

METHODS

We established a set of fluorescent PCR probes and primers for the definition of individual gene expression profiles of 12 different Eph receptors and 8 ephrins in 13 different healthy tissues. The mRNA expression profiles were studied in human lung, colorectal, kidney, liver, and brain cancers.

RESULTS

The family of Eph receptors/ephrins was widely expressed in adult tissues with organ-site-specific patterns: EphB6 was highest in the thymus, compatible with an involvement in T-cell maturation. Brain and testis shared a unique pattern with EphA6, EphA8, and EphB1 being the most prominent. EphA7 had a high abundance in the kidney vasculature. Ephrin-A3 was up-regulated 26-fold in lung cancer, and EphB2 was up-regulated 9-fold in hepatocellular carcinoma. EphA8 was down-regulated in colon cancer, and EphA1/EphA8 was down-regulated in glioblastomas.

CONCLUSION

Eph/Ephrin genes are widely expressed in all adult organs with certain organ-site-specific patterns. Because their function in adult tissues remains unknown, further analysis of their role in disease may disclose new insights beyond their well-defined meaning in development.

Heterogeneous expression and association of beta-catenin, p16 and c-myc in multistage colorectal tumorigenesis and progression detected by tissue microarray

Most colorectal carcinomas (CRCs) arise from adenomas through an archetypal pathogenic pathway, the adenoma-carcinoma-metastasis sequence. Aberrant expression of beta-catenin, p16, E-cadherin and c-myc appears to have played important roles in the development and/or progression of CRC, but their precise distribution pattern and associations in different pathologic loci along CRC's pathogenic pathway have not been thoroughly examined. In this study, a tissue microarray (TMA) containing 85 advanced CRCs in different Dukes stages was constructed. In each of 85 cases, tissue specimens from normal mucosa and primary carcinomas in different layers of the bowel wall were included in the TMA. Tissue specimens from matched adenoma, lymph node metastases and distant metastases were obtained from 22, 21 and 21 cases, respectively. Expression patterns of beta-catenin, p16, E-cadherin and c-myc were evaluated by immunohistochemistry. The results revealed that nuclear expression of beta-catenin, p16 and c-myc was quantitatively increased from normal mucosa to premalignant adenoma, primary carcinoma and lymph node metastatic carcinoma; the frequency of nuclear overexpression of beta-catenin and p16 in lymph node metastases was significantly higher than that in distant metastases (p < 0.05). These results suggest an association between nuclear overexpression of beta-catenin and/or p16 and CRC lymph node metastasis but not distant metastasis. The results also showed that correlative high nuclear expression of beta-catenin and c-myc was observed in primary carcinomas involving the serosa and lymph node metastases (p < 0.05) but not in other pathologic regions of CRCs, suggesting that the tumor microenvironment in different pathologic loci of colorectal tumorigenesis and progression may influence c-myc responsiveness to beta-catenin/Tcf activation.

Cytokine-regulated expression of collagenase-2 (MMP-8) is involved in the progression of ovarian cancer

Matrix metalloproteinases (MMPs) have been implicated in ovarian cancer progression. Among them, MMP-8 that degrades type I collagen may play a crucial role. The aim of our study was to determine MMP-8 expression and regulation in ovarian cancer and its association with other MMPs and tissue inhibitors of metalloproteinases (TIMPs). Tissue microarrays (TMAs) containing tissue cylinders from 302 patients were used for immunohistochemical studies. In addition, MMP-8 expression in vitro was analysed by a specific immunoassay and PCR-analysis. MMP-7 (81%), MMP-8 (95%), MT3-MMP (100%), TIMP-2 (100%), and TIMP-3 (96%) were expressed in all the OVCAs, but the staining intensities varied. MMP-3 (6%), MMP-9 (57%) and TIMP-1 (43%) expressions were more rarely detected. Only MMP-8 expression levels correlated with tumour grade (P<0.01), tumour stage (P<0.01), and a poor prognosis (P<0.05). MMP-8 protein and gene expression in vitro was found to be significantly upregulated by interleukin-1beta (IL-1beta, P<0.01). The data indicate that MMP-8 overexpression in OVCAs is regulated by IL-1beta and that pro-inflammatory cytokines may promote the invasive potential of ovarian cancer.

Expression of CEACAM6 in resectable colorectal cancer: a factor of independent prognostic significance

PURPOSE

CEACAM6, CEACAM1, and human carcinoembryonic antigen (CEA) are coexpressed in normal colorectal epithelia, but show deregulated expression in colorectal cancers (CRC). Upregulation of CEACAM6 expression in hyperplastic polyps and early adenomas represents one of the earliest observable molecular events leading to colorectal tumors. The aim of our study was to evaluate the prognostic relevance of CEACAM6, CEACAM1, and CEA tissue expression in patients with CRC.

PATIENTS AND METHODS

Immunohistochemical analysis was carried out on tissue microarrays from 243 paraffin-embedded biopsies from a randomized controlled clinical trial (Swiss Group for Clinical Cancer Research [SAKK] 40/81) of adjuvant fluorouracil-based chemotherapy with CEACAM-specific monoclonal antibodies. The median follow-up was 8 years. Overall survival (OS) and disease-free survival (DFS) were calculated using Kaplan-Meier estimates and hazard ratios (HRs) estimated using Cox proportional hazards models.

RESULTS

Tissue expression of CEACAM6, CEACAM1, and CEA was enhanced in 55%, 58%, and 94% of patients, respectively. Multivariate Cox analysis including sex, age, tumor site, stage, differentiation grade, treatment, and nodal status as covariates showed that CEACAM6 overexpression independently predicted poor OS (HR, 1.86; P =.0100) and DFS (HR, 2.00; P =.0028), whereas CEACAM1 or CEA were not significantly related to these outcomes. The data did not provide evidence for or against the hypothesis that the CEACAM6 effect on survival differs according to treatment.

CONCLUSION

Expression of the cell adhesion molecule CEACAM6 in CRC is an independent prognostic factor allowing subdivision of patients into low- and high-risk groups. Whether CEACAM6 or CEA and CEACAM1 might be useful as predictive markers of chemotherapy benefit remains unclear.

Calretinin expression in human normal and neoplastic tissues: a tissue microarray analysis on 5233 tissue samples

Calretinin is a calcium-binding protein expressed in different normal and neoplastic tissues. Early studies suggested that calretinin is a useful marker to differentiate adenocarcinomas from malignant mesotheliomas of the lung, but subsequent work has shown that calretinin can be expressed in several other tumor types. To systematically investigate the epidemiology of calretinin expression in normal and neoplastic tissues, we used tissue microarrays (TMAs) to analyze the immunohistochemically detectable expression of calretinin in 5233 tissue samples from 128 different tumor categories and 76 different normal tissue types. At least 1 case with weak expression could be found in 74 of 128 (58%) different tumor types and 46 entities (36%) had at least 1 tumor with strong positivity. In normal tissues, a particularly strong expression was found in Leydig cells of the testis, neurons of the brain, theca-lutein and theca interna cells of the ovary, and mesothelium. In tumors, strong calretinin expression was most frequently found in malignant mesotheliomas (6 of 7), Leydig cell tumors of the testis (5 of 5), adenomas of adrenal gland (5 of 9), and adenomatoid tumors (4 of 9). In summary, calretinin is frequently expressed in many different tumor types. Metastases of various different origins must be included in the differential diagnosis of calretinin-positive pleura tumors.

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.

Immunohistochemical analysis of B-cell lymphoma using tissue microarrays identifies particular phenotypic profiles of B-cell lymphomas

AIMS

To validate the applicability of tissue microarray (TM) in immunohistochemical profiling of B-cell lymphoma and to identify particular phenotypic profiles of B-cell neoplasms.

METHODS AND RESULTS

Eighty-two diffuse large B-cell lymphomas (DLBL), 54 follicular lymphomas (FL) and 74 mantle cell lymphomas (MCL) were arrayed. Immunohistochemical stains of TM were compared with immunostains of conventional, formalin-fixed and frozen material sections. Concordant staining results were obtained in more than 88% of cases for CD20, CD3, CD5, CD10, CD23, Bcl-2, IgD, secretory differentiation, p53 and p21 expression. Prognostically relevant hot-spot expression of Ki67 yielded concordant results in 71%. Applying TM for characterization of p27KIP1 expression, both typical and blastoid MCL only rarely showed p27KIP1 expression (9% and 15%), whereas 32% of nodal DLBL were p27KIP1-positive, irrespective of high proliferative activity. Among 22 B-cell lymphomas investigated genetically, a p53 + p21- immunophenotype in >20% of tumour cells correlated with p53 locus deletion.

CONCLUSIONS

Lymphoma TM allows for immunohistochemical profiling of human B-cell lymphoma with a comparable accuracy to immunohistochemical studies performed on conventional tissue sections. Nodal DLBLs showed significantly more frequent expression of IgD and p27KIP1 than extranodal DLBL. MCL and DLBL frequently showed aberrant p27KIP1 expression. A p53 + p21- immunophenotype in >20% of tumour cells in B-cell non-Hodgkin's lymphoma correlates with p53 gene deletion.

Tissue microarray technology: validation in colorectal carcinoma and analysis of p53, hMLH1, and hMSH2 immunohistochemical expression

Tissue microarray technology enables the analysis of hundreds of specimens by arranging numerous 0.6-mm tissue core biopsy specimens into a single paraffin block. Validation studies are necessary to evaluate the representativeness of small disks taken from the original tissue. We validated the tissue microarray technology in colorectal carcinoma by analyzing the immunohistochemical expression of proteins involved in the two main pathways of colorectal carcinogenesis: p53 protein for loss of heterozygosity tumors, hMLH1 and hMSH2 proteins for microsatellite instability (MSI) tumors. We compared in 30 colorectal carcinomas (15 MSI(-) and 15 MSI(+)), 8 microarrays disks, and the whole section of the block from which they were derived. Tumoral tissue was present in 95.7% of the microarray disks. The analysis of three disks per case was comparable to the analysis of the whole section in 99.6% (p53), 98.8% (hMLH1), and 99.2% (hMSH2) of cases. In the second part we applied the tissue microarray technology to 263 consecutive cases of colorectal carcinoma, sampled by three cores. We showed that 48.5% overexpressed p53 and 8.7% lost hMLH1 or hMSH2. Tissue microarray technology, validated in colorectal carcinoma, appears as a useful research tool for rapid analysis of the clinical interest of molecular alterations.

Quantitative analysis of colorectal tissue microarrays by immunofluorescence and in situ hybridization

The accuracy and reliability of in situ studies may be compromised by qualitative interpretations. Quantitation imposes a greater degree of objectivity, is more reproducible, and facilitates the clarity of definitions. The aim of this study was to validate the utility of laser imaging systems for the in situ quantitative analysis of gene expression in tissue microarrays. Immunofluorescence was employed to quantify the expression of the tumour suppressor p53, a marker of proliferation (Ki67), an endothelial cell marker (CD31), and the mismatch repair proteins human Mut L homologue 1 and human Mut S homologue 2 in an arrayed series of colorectal tissues (n = 110). Quantitative data on this panel of antigens were compared objectively with qualitative scoring of immunohistochemical chromogen deposition. In addition, the expression of vascular endothelial growth factor (VEGF)-A, placental growth factor, hepatocyte growth factor, and c-Met mRNA was quantified by phosphor image analysis of in situ hybridization reactions. The quantified data on p53, Ki67, and CD31 expression were significantly associated with the pathologist's score (p < or = 0.001). While hepatocyte growth factor and placental growth factor were not up-regulated, c-Met expression was increased up to 2.5-fold and the median VEGF-A expression was elevated 4-fold (p = 0.003) in this series of colorectal tumours. Laser imaging systems are therefore feasible for high-throughput, quantitative profiling of tissue microarrays.

Demystified...tissue microarray technology

Several "high throughput methods" have been introduced into research and routine laboratories during the past decade. Providing a new approach to the analysis of genomic alterations and RNA or protein expression patterns, these new techniques generate a plethora of new data in a relatively short time, and promise to deliver clues to the diagnosis and treatment of human cancer. Along with these revolutionary developments, new tools for the interpretation of these large sets of data became necessary and are now widely available. Tissue microarray (TMA) technology is one of these new tools. It is based on the idea of applying miniaturisation and a high throughput approach to the analysis of intact tissues. The potential and the scientific value of TMAs in modern research have been demonstrated in a logarithmically increasing number of studies. The spectrum for additional applications is widening rapidly, and comprises quality control in histotechnology, longterm tissue banking, and the continuing education of pathologists. This review covers the basic technical aspects of TMA production and discusses the current and potential future applications of TMA technology.

Analysis of the PI-3-Kinase-PTEN-AKT pathway in human lymphoma and leukemia using a cell line microarray

Tissue microarray technology facilitates rapid assessment of expression of molecular markers by enabling the simultaneous analysis of hundreds of tissue specimens. We have applied this technology to establish a microarray composed of cell pellets derived from 40 human lymphoma/leukemia-derived cell lines harboring a variety of molecular abnormalities. The application of cell line microarrays to the assessment of biologic marker evaluation was validated by studying the immunohistochemical expression of PTEN and phosphorylated AKT, two mediators of the phosphatidylinositol (PI)-3-kinase pathway. In addition to the high throughout analysis of protein expression in lymphoma/leukemia cells, this methodology also enables the evaluation of subcellular localization of protein expression. Cytoplasmic PTEN expression was observed in the majority of cell lines (87%), whereas a minor subset demonstrated nuclear expression. Phosphorylated AKT was also expressed predominantly within the cytoplasm in 65% of cell lines, whereas nuclear expression was seen in a minority. An inverse relationship between PTEN and phosphorylated AKT was observed in 63% of cell lines. No cell lines showed absence of PTEN expression, whereas 50% of cell lines showed low PTEN expression. Our data support the integrity of the PI-3-kinase-PTEN-AKT pathway in a majority of cell lines derived from hematologic malignancies and clearly demonstrates the utility of microarray technology in the in situ assessment of expression of molecular markers in tumor-derived cell lines.

Expression of NKX3.1 in normal and malignant tissues

BACKGROUND

NKX3.1, a member of the NK-class of homeodomain proteins, is expressed primarily in the adult prostate and has growth suppression and differentiating effects in prostate epithelial cells.

METHODS

We performed immunohistochemical analysis for NKX3.1 and PSA expression in 4,061 samples included in a tissue microarray of a broad spectrum of human cancers and normal tissues.

RESULTS

NKX3.1 expression was seen in prostate epithelial cells, prostate cancer, normal testis, 9% of primary and 5% of metastatic infiltrating ductal breast carcinoma, and 27% of primary and 26% of metastatic infiltrating lobular breast carcinoma. In a cohort of 474 primary breast cancers with median follow-up over 62.5 month survival, we found no effect of NKX3.1 expression on prognosis. NKX3.1 expression was more restricted than the spectrum of prostate specific antigen expression.

CONCLUSIONS

Expression of NKX3.1 is highly restricted and is found primarily in benign and malignant prostatic epithelial cells and also in normal testis and lobular carcinoma of the breast.

Tissue microarray analysis reveals prognostic significance of syndecan-1 expression in prostate cancer

BACKGROUND

Tissue microarrays (TMA) have recently emerged as powerful tools to rapidly analyze the clinical significance of new molecular markers in human tumors. Here, we have tested several molecular markers on a prostate TMA containing 637 different specimens.

METHODS

The specimens were from 551 patients with prostate cancer and long-term follow-up information on progression (median 5.3 years), tumor-specific and overall survival (median 5.9 years). Eighty-six specimens from benign prostatic hyperplasia were included as controls. Expression of Ki67, Bcl-2, p53, CD-10 (neutral endopeptidase), and syndecan-1 (CD-138) was analyzed by immunohistochemistry.

RESULTS

Gleason grade and Ki67 Labeling Index (LI) were independent predictors of early recurrence and poor survival. Bcl-2 predicted early recurrence, whereas p53 was associated with poor survival. Syndecan-1 overexpression also predicted early recurrence and was significantly associated with tumor specific survival, high Gleason grade, Ki67 LI, and Bcl-2 overexpression. Neoadjuvant hormonal therapy was associated with overexpression of Bcl-2 and inhibition of Ki67 LI and CD-10, but did not affect the expression of the remaining markers.

CONCLUSIONS

The results of this TMA study confirm a dominant prognostic significance of Gleason grading and Ki67 LI in prostate cancer, as compared to a less pronounced role of Bcl-2, and p53. We identified syndecan-1 as a new prognostic factor and provide evidence for an androgen-dependent regulation of CD-10 expression.

Genetics of endometriosis

Endometriosis long has been recognized as showing heritable tendencies, with recurrence risks of 5% to 7% for first-degree relatives. The risk indicates that polygenic and multifactorial etiology is far more likely to be the cause than mendelian inheritance. The current task is to determine the number and location of genes responsible for endometriosis. Molecular advances of the past decade make identification and elucidation of these genes a reality. The authors review the basis for concluding that endometriosis is a genetic disorder of polygenic/multifactorial inheritance. Genome-wide strategies for identifying causative genes are considered and available data on association or linkage to putative candidate genes systematically reviewed.

Conventional and tissue microarray immunohistochemical expression analysis of mismatch repair in hereditary colorectal tumors

Immunohistochemistry (IHC) of mismatch repair (MMR) proteins in colorectal tumors together with microsatellite analysis (MSI) can be helpful in identifying families eligible for mutation analysis. The aims were to determine sensitivity of IHC for MLH1, MSH2, and MSH6 and MSI analysis in tumors from known MMR gene mutation carriers; and to evaluate the use of tissue microarrays for IHC (IHC-TMA) of colon tumors in its ability to identify potential carriers of MMR gene mutations, and compare it with IHC on whole slides. IHC on whole slides was performed in colorectal tumors from 45 carriers of a germline mutation in one of the MMR genes. The TMA cohort consisted of 129 colon tumors from (suspected) hereditary nonpolyposis colorectal cancer (HNPCC) patients. Whole slide IHC analysis had a sensitivity of 89% in detecting MMR deficiency in carriers of a pathogenic MMR mutation. Sensitivity by MSI analysis was 93%. IHC can also be used to predict which gene is expected to harbor the mutation: for MLH1, MSH2, and MSH6, IHC on whole slides would have correctly predicted the mutation in 48%, 92%, and 75% of the cases, respectively. We propose a scheme for the diagnostic approach of families with (suspected) HNPCC. Comparison of the IHC results based on whole slides versus TMA, showed a concordance of 85%, 95%, and 75% for MLH, MSH2, and MSH6, respectively. This study therefore shows that IHC-TMA can be reliably used to simultaneously screen a large number of tumors from (suspected) HNPCC patients, at first in a research setting.

Symposium part 2: Should the Bethesda System terminology be used in diagnostic surgical pathology?: Counterpoint

The criteria currently used for grading cervical intraepithelial neoplasia (CIN) are arbitrary and subjective with consequent considerable intra- and interobserver variability. None of the currently used criteria make a clear-cut case for changing terminology. The combination of CIN 2 and CIN 3 into a high-grade lesion is not supported by biologic behavior or HPV typing and leads to overtreatment. The various shifts in nomenclature over the last 50 years through the dysplasia, CIN, and Bethesda systems, although intellectually stimulating, have neither improved diagnostic accuracy nor patient management. On the contrary, they often caused confusion and duplication, leading to the common and ironic practice that several terminologies are now being used in an additive fashion. New diagnostic markers are on the horizon as a result of the rapid development in the areas of genomics and proteomics. It seems likely that specific molecular biomarkers will become available, allowing the consistent and accurate discrimination between those intraepithelial lesions that will ultimately become invasive from the vast majority of lesions that will regress or persist. It is preferable at this time to maintain the current three-tier system, which is well entrenched and accepted around the world, until a novel approach places the classification of cervical precursor lesions on a new and solid footing. Ideally, we will then have a single-tier system identifying reliably those lesions that have the potential to become invasive.

Heritability and candidate genes for endometriosis

Endometriosis is inherited in polygenic/multifactorial fashion, with recurrence risks of 5-7% for first-degree relatives. The current task is to determine the number and location of causative genes. This review initially supports the basis for polygenic/multifactorial inheritance and then outlines genome-wide strategies for identifying causative genes. Potential candidate genes are surveyed, and discrepant results emphasized. Finally, a hypothesis for endometriosis, having a multi-step pathogenesis analogous to the pathogenesis of neoplasia, is considered.

Diffuse large B-cell lymphoma: one or more entities? Present controversies and possible tools for its subclassification

Diffuse large B-cell lymphoma (DLBCL) is the commonest type of lymphoid tumour world-wide. This category was included both in the REAL and WHO Classification aiming to lump together all malignant lymphomas characterized by the large size of the neoplastic cells, B-cell derivation, aggressive clinical presentation, and the need for highly effective chemotherapy regimens. These tumours are detected as primary or secondary forms both at the nodal and extranodal levels, in immunocompetent hosts as well as in patients with different types of immunosuppression. They display a significant variability in terms of cell morphology and clinical findings, which justifies the identification of variants and subtypes. Among the latter, the primary mediastinal one does actually correspond to a distinct clinicopathological entity. Immunophenotypic, tissue microarray and molecular studies underline the extreme heterogeneity of DLBCLs and suggest a subclassification of the tumour, based on the identification of different pathogenic pathways, which might have much greater relevance than pure morphology for precise prognostic previsions and adoption of ad hoc therapies. The more recent acquisitions on the pathobiology of DLBCLs are reviewed in the light of the authors' experience, aiming to contribute to the existing debate on the topic.

Tissue microarrays in the study of non-neoplastic disease of the nervous system

Tissue microarrays (TMAs), also known as "tissue chips," are a recently developed method that allows small cores or discs of tissue from dozens or hundreds of (usually paraffin-embedded) specimens to be re-embedded in a tissue block, which can then be further sectioned. The tissue cores can subsequently be studied using any combination of techniques, including immunohistochemistry, in situ hybridization (ISH). fluorescence ISH, and in situ polymerase chain reaction (PCR). To date, the technique has found greatest use in the analysis of neoplasms, including gliomas. We describe, and provide examples of, how TMAs might be utilized in investigation of autopsy (or biopsy) tissues from individuals with non-neoplastic disease, especially to address questions that require systematic review of multiple (nearly) identical brain regions across dozens or hundreds of cases. Specific questions related to patterns of protein expression (e.g. tau, Abeta, alpha-synuclein) in multiple regions of large numbers of brain specimens (from patients with neurodegenerative diseases) can be efficiently examined using TMA technology. One possible use of TMAs in the area of infectious disease might be to examine patterns of HIV-related brain injury or AIDS-related opportunistic CNS infections in the epochs before and after highly active antiretroviral therapy came into widespread use.

Detection of novel gene expression in paraffin-embedded tissues by isotopic in situ hybridization in tissue microarrays

Correlating altered gene expression patterns with particular disease states is a critical step in understanding disease processes and developing treatment strategies. Many thousands of novel gene sequences have recently been annotated in public and private databases and are now available for analysis. Tissue-specific expression patterns of these sequences can be evaluated physically on DNA arrays and other high throughput assays, or virtually by bioinformatics mining of expressed sequence tag (EST) databases. As a secondary screening tool, in situ hybridisation (ISH) not only confirms tissue specificity, but also reveals what is often valuable information about cell-type expression patterns of nov16l sequences. Due to their availability and long-term stability at room temperature, formalin-fixed paraffin-embedded clinical specimens provide an invaluable resource for evaluating expression patterns of novel human genes. We describe a high-throughput approach for identifying and quantifying the expression of novel genes in paraffin-embedded human tissues using isotopic in situ hybridisation and tissue microarrays (TMA).

Use of laser capture microdissection, cDNA microarrays, and tissue microarrays in advancing our understanding of prostate cancer

One difficulty in studying epithelial tumors has been the inability to isolate pure samples for DNA and RNA analysis. Prostate cancer, with its infiltrative nature, is particularly challenging. The Combination of several new technologies should help overcome these hurdles. Laser capture microdissection uses a laser beam to achieve transfer of pure cell populations for isolation of DNA, RNA, and protein. High-throughput analysis of these samples can be achieved by using cDNA expression microarrays. High-density tissue microarrays should allow for validation of differentially expressed genes. This review will concentrate on the application of laser capture microdissection, cDNA microarrays, and tissue microarrays in the area of prostate cancer research.