Applications of microarrays to histopathology

Role of Advanced Diagnostic Aids in the Detection of Potentially Malignant Disorders and Oral Cancer at an Early Stage

One of the most prevalent malignancies diagnosed today is cancer of the mouth or oral cancer. Compared to systemic malignancies like lung cancer, colon cancer, etc., oral cancer tends to get less attention from the general public. However, these lesions may be lethal if not treated, even if diagnosed early. Early diagnosis improves the prognosis for successful therapy. Delayed diagnosis is hypothesized to be a pivotal contributor to the dismal oral cancer survival rate over five years. The current standard of care for diagnosis and detection is based on clinical evaluation, the histological study of biopsy material, and genetic methods. There have been several advancements in the diagnostic technologies available to detect oral cancer at the initial phase. This study aims to dissect the cutting-edge methods for detecting oral cancer in its earliest stages.

Expression of estrogen and progesterone receptors, HER2 protein and Ki-67 proliferation index in breast carcinoma in both tumor tissue and tissue microarray

Breast cancer treatment is tailored to molecular subtypes, which are classified by cell type and by presence of estrogen and progesterone receptors, HER2 overexpression and Ki-67 proliferation index. In routine pathological practice, these markers are detected in tumor tissue using immunohistochemistry, which requires four immunohistochemical antibodies for each patient. We developed a new tissue microarray procedure using a punch device with a 6 mm core diameter. The presence of estrogen and progesterone receptors, HER2 expression and the Ki-67 proliferation index of tumor tissues of 50 breast carcinoma patients had been determined using the conventional approach. We created three tissue microarray blocks, each containing samples from 14 main tumor tissues. One tissue microarray block was created with samples taken from eight main tumor tissues. Sections were cut from the four blocks and subjected to immunohistochemical staining; the original samples and the microarrays then were compared. We found significant agreement between estrogen receptor, progesterone receptor and HER-2 expression as well as Ki-67 proliferation index status of the original tumor tissues and the tissue microarray. Our tissue microarray technique using a single 6 mm core is a reliable and cost-effective method for determining estrogen and progesterone receptors, HER-2 status and Ki-67 proliferation index levels in patients with early breast carcinoma.

Tissue-Specific Expression of the Low-Affinity IgG Receptor, FcγRIIb, on Human Mast Cells

Immediate hypersensitivity reactions are induced by the interaction of allergens with specific IgE antibodies bound via FcεRI to mast cells and basophils. While these specific IgE antibodies are needed to trigger such reactions, not all individuals harboring IgE exhibit symptoms of allergy. The lack of responsiveness seen in some subjects correlates with the presence of IgG antibodies of the same specificity. In cell culture studies and in vivo animal models of food allergy and anaphylaxis such IgG antibodies have been shown to exert suppression via FcγRIIb. However, the reported absence of this inhibitory receptor on primary mast cells derived from human skin has raised questions about the role of IgG-mediated inhibition of immediate hypersensitivity in human subjects. Here, we tested the hypothesis that mast cell FcγRIIb expression might be tissue specific. Utilizing a combination of flow cytometry, quantitative PCR, and immunofluorescence staining of mast cells derived from the tissues of humanized mice, human skin, or in fixed paraffin-embedded sections of human tissues, we confirm that FcγRIIb is absent from dermal mast cells but is expressed by mast cells throughout the gastrointestinal tract. IgE-induced systemic anaphylaxis in humanized mice is strongly inhibited by antigen-specific IgG. These findings support the concept that IgG, signaling via FcγRIIb, plays a physiological role in suppressing hypersensitivity reactions.

Downregulation of TAP1 and TAP2 in early stage breast cancer

TAP1-TAP2 heterodimeric complexes are recognized as the transporter associated with antigen processing of major histocompatibility complex class I peptides for recognition by tumor-specific cytotoxic T lymphocytes. In this study, we investigated the immunohistochemical expression of TAP1 and TAP2 in 160 patients with breast cancer and correlated their expression levels with clinicopathologic parameters. The median age of the patient cohort was 52.5 years (range, 30–86 years). Both TAP1 and TAP2 immunohistochemical expression levels correlated significantly with breast cancer characteristics (P < .001). TAP1 expression levels were low to negative in stage I breast tumors. TAP1 and TAP2 levels were significantly higher in grade 3 tumors than low-grade (grade 1 and 2) tumors. TAP1 and TAP2 expression levels were not significantly different among different levels of HER2-expressing tumors and did not vary by estrogen and progesterone receptor status or patient age. Both TAP1 and TAP2 overexpression in breast cancer might be an indicator of an aggressive breast tumor.

BRCA2 carriers with male breast cancer show elevated tumour methylation

Background

Male breast cancer (MBC) represents a poorly characterised group of tumours, the management of which is largely based on practices established for female breast cancer. However, recent studies demonstrate biological and molecular differences likely to impact on tumour behaviour and therefore patient outcome. The aim of this study was to investigate methylation of a panel of commonly methylated breast cancer genes in familial MBCs.

Methods

60 tumours from 3 BRCA1 and 25 BRCA2 male mutation carriers and 32 males from BRCAX families were assessed for promoter methylation by methylation-sensitive high resolution melting in a panel of 10 genes (RASSF1A, TWIST1, APC, WIF1, MAL, RARβ, CDH1, RUNX3, FOXC1 and GSTP1). An average methylation index (AMI) was calculated for each case comprising the average of the methylation of the 10 genes tested as an indicator of overall tumour promoter region methylation. Promoter hypermethylation and AMI were correlated with BRCA carrier mutation status and clinicopathological parameters including tumour stage, grade, histological subtype and disease specific survival.

Results

Tumours arising in BRCA2 mutation carriers showed significantly higher methylation of candidate genes, than those arising in non-BRCA2 familial MBCs (average AMI 23.6 vs 16.6, p = 0.01, 45% of genes hypermethylated vs 34%, p < 0.01). RARβ methylation and AMI-high status were significantly associated with tumour size (p = 0.01 and p = 0.02 respectively), RUNX3 methylation with invasive carcinoma of no special type (94% vs 69%, p = 0.046) and RASSF1A methylation with coexistence of high grade ductal carcinoma in situ (33% vs 6%, p = 0.02). Cluster analysis showed MBCs arising in BRCA2 mutation carriers were characterised by RASSF1A, WIF1, RARβ and GTSP1 methylation (p = 0.02) whereas methylation in BRCAX tumours showed no clear clustering to particular genes. TWIST1 methylation (p = 0.001) and AMI (p = 0.01) were prognostic for disease specific survival.

Conclusions

Increased methylation defines a subset of familial MBC and with AMI may be a useful prognostic marker. Methylation might be predictive of response to novel therapeutics that are currently under investigation in other cancer types.

Electronic supplementary material

The online version of this article (10.1186/s12885-017-3632-7) contains supplementary material, which is available to authorized users.

Global Gene Expression Profiling: A Complement to Conventional Histopathologic Analysis of Neoplasia

Transcriptional profiling of entire tumors has yielded considerable insight into the molecular mechanisms of heterogeneous cell populations within different types of neoplasms. The data thus acquired can be further refined by microdissection methods that enable the analyses of subpopulations of neoplastic cells. Separation of the various components of a neoplasm (i.e., stromal cells, inflammatory infiltrates, and blood vessels) has been problematic, primarily because of a paucity of tools for accurate microdissection. The advent of laser capture microdissection combined with powerful tools of linear amplification of RNA and high-throughput microarray-based assays have allowed the transcriptional mapping of intricate and highly complex networks within pure populations of neoplastic cells. With this approach, specific “molecular signatures” can be assigned to tumors of distinct or even similar histomorphology, thereby aiding the desired objective of pattern recognition, tumor classification, and prognostication. This review highlights the potential benefits of global gene expression profiling of tumor cells as a complement to conventional histopathologic analyses.

Identification of CEACAM5 as a Biomarker for Prewarning and Prognosis in Gastric Cancer

MGd1, a monoclonal antibody raised against gastric cancer cells, possesses a high degree of specificity for gastric cancer (GC). Here we identified that the antigen of MGd1 is CEACAM5, and used MGd1 to investigate the expression of CEACAM5 in non-GC and GC tissues (N=643), as a biomarker for prewarning and prognosis. The expression of CEACAM5 was detected by immunohistochemistry in numerous tissues; its clinicopathological correlation was statistically analyzed. CEACAM5 expression was increased progressively from normal gastric mucosa to chronic atrophic gastritis, intestinal metaplasia, dysplasia and finally to GC (p<0.05). In gastric precancerous lesions (intestinal metaplasia and dysplasia), CEACAM5-positive patients had a higher risk of developing GC as compared with CEACAM5-negative patients (OR = 12.68, p<0.001). Besides, CEACAM5 was found positively correlated with invasion depth of gastric adenocarcinoma (p<0.001). In survival analysis, CEACAM5 was demonstrated to be an independent prognostic predictor for patients with GC of clinical stage IIIA/IV (p=0.033). Our results demonstrate that CEACAM5 is a promising biomarker for GC prewarning and prognostic evaluation.

Differential expression of immunohistochemical markers in primary lung and breast cancers enriched for triple-negative tumours

AIMS

In breast cancer patients presenting with a lung lesion, the distinction between lung and breast origin is clinically important. Lung and breast cancers are both CK7(+) /CK20(-) , so additional immunohistochemical markers are needed.

METHODS AND RESULTS

We examined the expression of oestrogen receptor (ER), progesterone receptor (PR), thyroid transcription factor-1 (TTF-1), gross cystic disease fluid protein-15 (GCDFP-15), p63 and Wilms' tumour 1 (WT1) in a series of tissue microarrays comprising 266 non-small-cell lung cancers and 837 primary breast cancers enriched for triple-negative tumours (TNBC). Staining for ER, PR, TTF-1 and GCDFP-15 was present in 63%, 49%, 0% and 25% of breast and 6%, 9%, 59% and 1% of lung cancers, respectively. Strong staining for p63 was present in 63 (97%) lung squamous cell carcinomas and only eight (9%) TNBC. WT1 nuclear staining was rare; however, cytoplasmic staining was identified in 49 (40%) TNBC and 10 (5%) lung cancers. Cluster analysis segregated TNBC from lung cancers with TTF-1 and/or p63 staining favouring lung origin, and GCDFP-15 or WT1 staining favouring breast origin. Cancers negative for all four markers (17%) were 60% breast and 40% lung origin.

CONCLUSION

An immunohistochemical panel incorporating ER, TTF-1, GCDFP-15, p63 and WT1 can help to distinguish lung cancer from metastatic breast cancer, including TNBC.

The use of tissue microarrays for semiquantitative evaluation of ATPaseC1 expression is ineffective

We described earlier the possible role of ATPaseC1 expression as a diagnostic and prognostic marker for oral cancer; others have reported its use for tumors of the lung and breast. We assessed ATPaseC1 expression in a sample of oral squamous cell carcinoma (OSCC) using tissue microarrays (TMAs) to analyze the relation between ATPaseC1 expression and clinical, histopathological and prognostic parameters. We performed a retrospective study of 48 cases of OSCC. We constructed TMAs using two different regions of each tumor. V-ATPaseC1 immunohistochemistry was performed and assessed semiquantitatively. ATPaseC1 staining was observed in most of the neoplastic cells in all tumors. Staining was diffusely cytoplasmic and, to a lesser extent, nuclear. The degree of concordance between the measurements performed in tissue microarray 1 (TMA1) and tissue microarray 2 (TMA2), as evaluated using the intra-class correlation coefficient (ICC), was low. We found great variability in the immunohistochemical staining of the different regions of each tumor. We found 16 cases with mild expression (33.3%), 20 with moderate expression (41.7%) and 12 with intense expression (25%). Differences in the clinical-pathological variables studied were not statistically significant. The difficulty of immunohistochemical evaluation, the heterogeneity of the carcinomas and the fact that evaluation of expression requires semiquantitative analysis render the reliability of the results obtained from TMA-based techniques questionable.

Mutational profiling of familial male breast cancers reveals similarities with luminal A female breast cancer with rare TP53 mutations

Background:

Male breast cancer (MBC) is still poorly understood with a large proportion arising in families with a history of breast cancer. Genomic studies have focused on germline determinants of MBC risk, with minimal knowledge of somatic changes in these cancers.

Methods:

Using a TruSeq amplicon cancer panel, this study evaluated 48 familial MBCs (3 BRCA1 germline mutant, 17 BRCA2 germline mutant and 28 BRCAX) for hotspot somatic mutations and copy number changes in 48 common cancer genes.

Results:

Twelve missense mutations included nine PIK3CA mutations (seven in BRCAX patients), two TP53 mutations (both in BRCA2 patients) and one PTEN mutation. Common gains were seen in GNAS (34.1%) and losses were seen in GNAQ (36.4%), ABL1 (47.7%) and ATM (34.1%). Gains of HRAS (37.5% vs 3%, P=0.006), STK11 (25.0% vs 0%, P=0.01) and SMARCB1 (18.8% vs 0%, P=0.04) and the loss of RB1 (43.8% vs 13%, P=0.03) were specific to BRCA2 tumours.

Conclusions:

This study is the first to perform high-throughput somatic sequencing on familial MBCs. Overall, PIK3CA mutations are most commonly seen, with fewer TP53 and PTEN mutations, similar to the profile seen in luminal A female breast cancers. Differences in mutation profiles and patterns of gene gains/losses are seen between BRCA2 (associated with TP53/PTEN mutations, loss of RB1 and gain of HRAS, STK11 and SMARCB1) and BRCAX (associated with PIK3CA mutations) tumours, suggesting that BRCA2 and BRCAX MBCs may be distinct and arise from different tumour pathways. This has implications on potential therapies, depending on the BRCA status of MBC patients.

Tissue microarray is a reliable method for immunohistochemical analysis of pleomorphic adenoma

OBJECTIVE

To determine the most adequate number and size of tissue microarray (TMA) cores for pleomorphic adenoma immunohistochemical studies.

STUDY DESIGN

Eighty-two pleomorphic adenoma cases were distributed in 3 TMA blocks assembled in triplicate containing 1.0-, 2.0-, and 3.0-mm cores. Immunohistochemical analysis against cytokeratin 7, Ki67, p63, and CD34 were performed and subsequently evaluated with PixelCount, nuclear, and microvessel software applications.

RESULTS

The 1.0-mm TMA presented lower results than 2.0- and 3.0-mm TMAs versus conventional whole section slides. Possibly because of an increased amount of stromal tissue, 3.0-mm cores presented a higher microvessel density. Comparing the results obtained with one, two, and three 2.0-mm cores, there was no difference between triplicate or duplicate TMAs and a single-core TMA.

CONCLUSIONS

Considering the possible loss of cylinders during immunohistochemical reactions, 2.0-mm TMAs in duplicate are a more reliable approach for pleomorphic adenoma immunohistochemical study.

Tissue microarrays: fast-tracking protein expression at the cellular level

Tissue microarrays maximize returns in cellular pathology whilst minimizing the use of cells and tissues. They are made by arraying cores of tissue taken from multiple donor blocks into a single recipient block. Accordingly, the histology and pathology of several hundred tissues can be represented in one tissue microarray that, when stained by immunohistochemistry, provides comprehensive topographic information on protein expression. Used with complimentary techniques, such as complementary DNA microarray analysis, tissue microarrays are providing valuable data for the identification of new markers of disease and assisting in the discovery of therapeutic targets. They are also leading a revolution in cellular pathology as high-throughput technology is introduced to maximize the information provided.

When tissue antigens and antibodies get along: revisiting the technical aspects of immunohistochemistry--the red, brown, and blue technique

Once focused mainly on the characterization of neoplasms, immunohistochemistry (IHC) today is used in the investigation of a broad range of disease processes with applications in diagnosis, prognostication, therapeutic decisions to tailor treatment to an individual patient, and investigations into the pathogenesis of disease. This review addresses the technical aspects of immunohistochemistry (and, to a lesser extent, immunocytochemistry) with attention to the antigen-antibody reaction, optimal fixation techniques, tissue processing considerations, antigen retrieval methods, detection systems, selection and use of an autostainer, standardization and validation of IHC tests, preparation of proper tissue and reagent controls, tissue microarrays and other high-throughput systems, quality assurance/quality control measures, interpretation of the IHC reaction, and reporting of results. It is now more important than ever, with these sophisticated applications, to standardize the entire IHC process from tissue collection through interpretation and reporting to minimize variability among laboratories and to facilitate quantification and interlaboratory comparison of IHC results.

Heart research advances using database search engines, Human Protein Atlas and the Sydney Heart Bank

This Methodological Review is intended as a guide for research students who may have just discovered a human "novel" cardiac protein, but it may also help hard-pressed reviewers of journal submissions on a "novel" protein reported in an animal model of human heart failure. Whether you are an expert or not, you may know little or nothing about this particular protein of interest. In this review we provide a strategic guide on how to proceed. We ask: How do you discover what has been published (even in an abstract or research report) about this protein? Everyone knows how to undertake literature searches using PubMed and Medline but these are usually encyclopaedic, often producing long lists of papers, most of which are either irrelevant or only vaguely relevant to your query. Relatively few will be aware of more advanced search engines such as Google Scholar and even fewer will know about Quertle. Next, we provide a strategy for discovering if your "novel" protein is expressed in the normal, healthy human heart, and if it is, we show you how to investigate its subcellular location. This can usually be achieved by visiting the website "Human Protein Atlas" without doing a single experiment. Finally, we provide a pathway to discovering if your protein of interest changes its expression level with heart failure/disease or with ageing.

Novel molecular imaging platform for monitoring oncological kinases

Recent advances in oncology have lead to identification of a plethora of alterations in signaling pathways that are critical to oncogenesis and propagation of malignancy. Among the biomarkers identified, dysregulated kinases and associated changes in signaling cascade received the lion's share of scientific attention and have been under extensive investigations with goal of targeting them for anti-cancer therapy. Discovery of new drugs is immensely facilitated by molecular imaging technology which enables non-invasive, real time, dynamic imaging and quantification of kinase activity. Here, we review recent development of novel kinase reporters based on conformation dependent complementation of firefly luciferase to monitor kinase activity. Such reporter system provides unique insights into the pharmacokinetics and pharmacodynamics of drugs that modulate kinase signaling and have a huge potential in drug discovery, validation, and drug-target interactions.

Molecular markers for detection, surveillance and prognostication of bladder cancer

Many markers for the detection of bladder cancers have been tested and almost all urinary markers reported are better than cytology with regard to sensitivity, but they score lower in specificity. Currently molecular and genetic changes play an important role in the discovery of new molecular markers for detection, prognostication and surveillance. The purpose of this review is to highlight the most important urinary molecular biomarker developments that have been studied and reported recently. In the current review we have summarized the most recent and relevant published reports on molecular urinary markers. The results of this review show that the first generation of urinary markers did not add much to urinary cytology. The current generation of markers is better, but additional clinical trials are needed. Our knowledge of molecular pathways in bladder cancer is growing and new methods of marker development emerge, but the perfect marker is still to be found. Currently, there are not clinically usable molecular markers that can guide us in diagnosis or surveillance, nor guide us in lowering the frequency of urethrocystoscopy in bladder cancer.

Avoiding Pitfalls in the Statistical Analysis of Heterogeneous Tumors

Information about tumors is usually obtained from a single assessment of a tumor sample, performed at some point in the course of the development and progression of the tumor, with patient characteristics being surrogates for natural history context. Differences between cells within individual tumors (intratumor heterogeneity) and between tumors of different patients (intertumor heterogeneity) may mean that a small sample is not representative of the tumor as a whole, particularly for solid tumors which are the focus of this paper. This issue is of increasing importance as high-throughput technologies generate large multi-feature data sets in the areas of genomics, proteomics, and image analysis. Three potential pitfalls in statistical analysis are discussed (sampling, cut-points, and validation) and suggestions are made about how to avoid these pitfalls.

Leptin expression correlates with favorable clinicopathologic phenotype and better prognosis in colorectal adenocarcinoma

Leptin, the product of the ob gene, is an adipocyte-derived neurohormone that regulates body fat storage and feeding behavior. Some studies have suggested that leptin has growth-factor-like functions in epithelial cells and its abnormal expression may be involved in cancer development and progression. We investigated leptin expression in normal and neoplastic colorectal tissues and its association with clinicopathological features and clinical outcome in colorectal adenocarcinoma patients. Leptin expression was evaluated on the tissue microarray of 44 normal colon mucosal tissues, 44 adenomatous polyps, and 437 colorectal adenocarcinomas by immunohistochemistry. Data were analyzed by chi-square test, one-way analysis of variance (ANOVA), Cox regression hazards model, and log-rank test with Kaplan-Meier curves. Frequency of leptin expression was dramatically increased from normal colonic mucosa (2/44, 4.5%) to adenomas (13/44, 29.5%) and adenocarcinomas (321/437, 73.5%) as neoplastic progression. Interestingly, leptin expression was correlated with favorable tumor features in depth of invasion (p = 0.033), lymph node metastasis (p = 0.019), American Joint Committee on Cancer (AJCC) and Dukes' stage (p = 0.021 and p = 0.005, respectively), differentiation (p = 0.010), and lymphatic invasion (p = 0.003). In univariate survival analysis, patients with leptin-positive adenocarcinoma revealed better overall and disease-free survivals (p = 0.032 and p = 0.004, respectively, log-rank test). In multivariate survival analysis with Cox proportional hazards model, leptin expression was an independent prognostic marker of disease-free survival (p = 0.009). We conclude that leptin was gradually expressed during the normal-adenoma-adenocarcinoma sequence, suggesting an association in colorectal carcinogenesis. In addition, high leptin expression was an indicator of favorable tumor features and better survival of colorectal cancer patients.

Prognostic value of signal transducers and activators of transcription 3 in breast cancer

INTRODUCTION

Constitutively activated signal transducers and activators of transcription (STAT) proteins are found in various types of tumors. However, there is still very limited information about the role of STATs in breast cancer. The power of tissue microarray technique is the capability of doing a series of analyses of thousands specimens in a parallel fashion with minimal damage to the origin blocks. This study was designed with the application of tissue microarray to analyze the STAT3 status in breast cancer.

MATERIALS AND METHODS

Archival tissue specimens from 102 patients with primary invasive breast cancer were selected, and STAT3 expression was analyzed by immunohistochemical staining with tissue microarray. The data of primary tumor staging, age, estrogen receptor status, lymph node status, histologic grading, and tumor-node-metastasis staging were also collected.

RESULTS

By multivariate analysis, the STAT3 expression turned out to be significantly related to the overall 5-year survival rate (P = 0.024).

CONCLUSION

Immunohistochemical staining with tissue microarray was convenient and feasible for the analysis of STAT3 expression status in breast cancer. Our preliminary results are promising and deserve further evaluation.

Biomarker validation: in situ analysis of protein expression using semiquantitative immunohistochemistry-based techniques

Biomarker-driven cancer research is common in the current literature. Much of this research is a result of the increase in genomic and proteomic high-throughput technologies, which have increased our knowledge and also produced an abundance of data with unclear clinical significance. Immunohistochemistry-based assessment of protein expression is a natural validation method of expression-profiling data that is easily performed on tissue samples collected prospectively or from archived samples. Coupled with tissue microarray technology and the increasing number of available automated, quantitative systems to read these arrays, we now have an efficient method of validating biomarkers for prognostic and predictive capabilities and for the identification of drug development targets.

Tissue microarrays from bone marrow aspirates for high-throughput assessment of immunohistologic markers in pediatric acute leukemia

Gene expression profiling studies have been employed to investigate prognostic subgroups in pediatric acute leukemia. Tissue microarrays (TMAs) are useful for high-throughput analysis of protein expression of target genes in acute leukemia samples and for validation of gene microarray analysis. Using cryopreserved samples of pediatric acute leukemia bone marrow aspirates, we constructed TMA from as few as 1 million cells. Bone marrow core biopsies from the same patients were included on the same TMA for comparison. A panel of 15 immunohistochemical markers typically used for diagnosis as well as those targeting recently characterized, prognostically relevant molecules of interest in pediatric acute leukemia was used to evaluate protein expression. Staining results confirm that suspension cells from bone marrow aspirates can be effectively used to derive protein expression data from multiple cases simultaneously with comparable efficacy to that of biopsy tissue. This method allows for new markers of diagnostic, prognostic, or therapeutic importance to be screened on large numbers of study patients. Furthermore, this technique may facilitate the inclusion of small samples, aspirates, and body fluids in large-scale studies of protein expression in clinical trials and protocols in which tissue biopsies are often unavailable.

Gene expression profiling of breast cancer

DNA microarray platforms for gene expression profiling were invented relatively recently, and breast cancer has been among the earliest and most intensely studied diseases using this technology. The molecular signatures so identified help reveal the biologic spectrum of breast cancers, provide diagnostic tools as well as prognostic and predictive gene signatures, and may identify new therapeutic targets. Data are best presented in an open access format to facilitate external validation, the most crucial step in identifying robust, reproducible gene signatures suitable for clinical translation. Clinically practical applications derived from full expression profile studies already in use include reduced versions of microarrays representing key discriminatory genes and therapeutic targets, quantitative polymerase chain reaction assays, or immunohistochemical surrogate panels (suitable for application to standard pathology blocks). Prospective trials are now underway to determine the value of such tools for clinical decision making in breast cancer; these efforts may serve as a model for using such approaches in other tumor types.

Tissue microarrays in clinical oncology

Tissue microarray (TMA) is a recently implemented, high-throughput technology for the analysis of molecular markers in oncology. This research tool permits the rapid assessment of a biomarker in thousands of tumor samples, using commonly available laboratory assays such as immunohistochemistry and in situ hybridization. Although introduced less than a decade ago, TMA has proven to be invaluable in the study of tumor biology, the development of diagnostic tests, and the investigation of oncologic biomarkers. This review describes the impact of TMA-based research in clinical oncology and its potential future applications. Technical aspects of TMA construction and the advantages and disadvantages inherent to this technology are also discussed.

Detection of micrometastases in pN0 non-small cell lung cancer: an alternative method combining tissue microarray and immunohistochemistry

OBJECTIVE

To present an alternative method of detecting micrometastases in lymph nodes previously testing negative for non-small cell lung cancer (NSCLC) by routine hematoxylin-eosin staining.

METHODS

A total of 77 hilar and mediastinal lymph nodes resected from 18 patients with NSCLC were investigated for the presence of micrometastases using a combination of microarray analysis and immunohistochemistry.

RESULTS

Micrometastases were detected by identifying cytokeratin- and chromogranin-positive cells in lymph node microarrays. Of the 18 patients initially staged as pN0 through routine hematoxylin-eosin staining, 9 (50%) were restaged as N1, and the prognoses were re-evaluated in terms of histological and clinical parameters. The comparison of the survival curves revealed that survival was higher in the patients without micrometastases than in those with micrometastases. In addition, in the multivariate analysis adjusted for age, gender, histological type, and restaging, the presence of micrometastases proved to be an independent predictor of survival. Among patients who had been previously staged as pN0, the risk of death was found to be 7-times greater for those later diagnosed with micrometastases than for those in whom no micrometastases were identified.

CONCLUSION

The combination of microarray analysis and immunohistochemistry might represent a low-cost and less time-consuming alternative for identifying occult micrometastases and predicting prognoses in surgically resected patients with pN0 NSCLC. Larger randomized, prospective studies are needed in order to determine the accuracy of this method.

Application of tissue microarrays in placental research

A complementary tool to gene-based arrays are tissue microarrays, which allow the validation of DNA/RNA-derived profiling results on the protein level and offer the possibility of exact location within the tissue structures. Here we describe the technical details of the application of tissue microarray in placental research. Although the placenta represents a very inhomogeneous organ, this technique is also usable in placental research.

Cell cycle regulators show diagnostic and prognostic utility for differentiated thyroid cancer

BACKGROUND

Differentiated thyroid cancer (DTC) generally has a favorable outcome, but some patients develop local recurrence and/or distant metastases and ultimately die of their disease. Molecular markers that accurately predict tumor behavior are lacking. This study's aim was to ascertain the role of cell cycle regulators in predicting malignant histology and tumor behavior in DTC.

METHODS

Tissue microarrays consisting of 100 benign and 105 malignant thyroid lesions, plus 24 lymph node samples, were stained for p16, p21, p27, p53, p57, p63, cyclin D1, cyclin E, and mdm2. Statistical analysis was used to compare the expression of the markers in benign versus DTC lesions and correlate their expression with clinicopathologic characteristics.

RESULTS

p16, p21, cyclin D1, and cyclin E showed significantly (P < .001) increased expression in DTCs compared with benign thyroid lesions (54.7% vs. 5%, 71.7% vs. 38%, 87.1% vs. 45.7%, and 72.3% vs. 37.4%, respectively). There was no significant difference in expression between benign lesions and DTC for the remaining markers. p16 expression correlated significantly with extrathyroidal tumor extension (P = .02) and the presence of cancer in lymph nodes (P = .03). A total of 73% vs. 45% of the cancers of patients with and without lymph node involvement, respectively, stained positive for p16 (P = .01).

CONCLUSIONS

There is a statistically significant difference in the expression of p16, p21, cyclin D1, and cyclin E between DTCs and benign thyroid lesions, and p16 expression correlates with clinicopathologic variables predicting poor outcomes for DTC. These results suggest that evaluation of cell cycle derangement in thyroid tumors may serve as a useful tool for both DTC diagnosis and prognosis.

Annotation and query of tissue microarray data using the NCI Thesaurus

Background

The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, specifying the pathological diagnoses for each sample. These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult.

Results

We developed methods to map these annotations to the NCI thesaurus. Using the NCI-T we can effectively represent annotations for about 86% of the samples. We demonstrate how this mapping enables ontology driven integration and querying of tissue microarray data. We have deployed the mapping and ontology driven querying tools at the TMAD site for general use.

Conclusion

We have demonstrated that we can effectively map the diagnosis-related terms describing a sample in TMAD to the NCI-T. The NCI thesaurus terms have a wide coverage and provide terms for about 86% of the samples. In our opinion the NCI thesaurus can facilitate integration of this resource with other biological data.

Screening of tissue microarrays for ubiquitin proteasome system components in tumors

The turnover of key proteins that mediate development, cellular proliferation, and a host of essential biological processes is controlled by the ubiquitin proteasome system (UPS). In several well-studied examples, notably in the cell cycle, regulatory proteins that control ubiquitin-dependent destruction are themselves substrates of the UPS, creating a multilayered system to ensure precise and dynamic control of protein stability. UPS regulators controlled at the level of protein stability--including the F-box protein Skp2 and the VHL protein (substrate adapter proteins for multicomponent E3 ubiquitin ligases)-- seem to be misregulated in tumors. In these cases, especially, measuring levels of critical regulatory and target proteins will often present a more biologically meaningful picture than examining relative mRNA levels, which do not always reflect corresponding protein levels. Tissue microarrays (TMAs) allow simultaneous screening of large numbers of tumors for expression of specific proteins by immunohistochemical staining of a single microscope slide prepared from a TMA paraffin block. Replicate slides prepared from the same block can be immunostained for multiple proteins functioning in a related pathway, and a semiquantitative protein expression profile for a given subset of UPS pathway components, or other subsets of proteins of interest, can be assembled. Protein expression profiles of individual tumors or tissue types can be compared and visualized by hierarchical clustering methods. These expression profiles may be used as screening tools to investigate the relative abundance of components of a biochemical pathway in tumors or other tissues. TMAs have an exciting future as tools for basic research, diagnostic pathology, and drug targeting. In this article, we provide an introduction to the use of TMAs to study the expression of UPS component proteins and substrates in tumors by immunohistochemistry.

Molecular targets in gynaecological cancers

The application of high throughput expression profiling and other advanced molecular biology laboratory techniques has revolutionised the management of cancers and is gaining attention in the field of gynaecological cancers. Such new approaches may help to improve our understanding of carcinogenesis and facilitate screening and early detection of gynaecological cancers and their precursors. Individualised prediction of patients' responses to therapy and design of personalised molecular targeted therapy is also possible. The studies of various molecular targets involved in the various signal pathways related to carcinogenesis are particularly relevant to such applications. At the moment, the application of detection and genotyping of human papillomavirus in management of cervical cancer is one of the most well established appliances of molecular targets in gynaecological cancers. Methylation, telomerase and clonality studies are also potentially useful, especially in assisting diagnosis of difficult clinical scenarios. This post-genomic era of clinical medicine will continue to make a significant impact in routine pathology practice. The contribution of pathologists is indispensable in analysis involving tissue microarray. On the other hand, both pathologists and bedside clinicians should be aware of the limitation of these molecular targets. Interpretation must be integrated with clinical and histopathological context to avoid misleading judgement. The importance of quality assurance of all such molecular techniques and their ethical implications cannot be over-emphasised.

Molecular profiling techniques and bioinformatics in cancer research

AIMS

Our aim was to describe the commonly used molecular profiling techniques in cancer research, to examine their limitations and to discuss the challenges of bioinformatics.

METHODS

A literature search was performed using the PubMed database to identify publications relevant to this review. Citations from these articles were also examined to yield further relevant publications.

RESULTS

We describe the use of DNA microarrays, comparative genomic hybridisation, tissue microarrays and digital differential display. The limitations of these technologies, their contribution to cancer research and the challenges of bioinformatics are also discussed.

CONCLUSIONS

Although these high throughput technologies each have their own limitations they are rapidly developing and contributing significantly to our understanding of cancer genetics. They have also led to the emergence of bioinformatics as a rapidly developing and vital field.

Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection

BACKGROUND

Chlamydophila pneumoniae infection has been implicated as a potential risk factor for atherosclerosis, however the mechanism leading to persistent infection and its role in the disease process remains to be elucidated.

METHODS

We validated the use of tissue microarray (TMA) technology, in combination with immunohistochemistry (IHC), to test antibodies (GroEL, GroES, GspD, Ndk and Pyk) raised against differentially expressed proteins under an interferon-gamma (IFN-gamma) induced model of chlamydial persistence.

RESULTS

In the cell pellet array, we were able to identify differences in protein expression patterns between untreated and IFN-gamma treated samples. Typical, large chlamydial inclusions could be observed in the untreated samples with all antibodies, whereas the number of inclusions were decreased and were smaller and atypical in shape in the IFN-gamma treated samples. The staining results obtained with the TMA method were generally similar to the changes observed between normal and IFN-gamma persistence using proteomic analysis. Subsequently, it was shown in a second TMA including archival atheromatous heart tissues from 12 patients undergoing heart transplantation, that GroEL, GroES, GspD and Pyk were expressed in atheromatous heart tissue specimens as well, and were detectable morphologically within lesions by IHC.

CONCLUSION

TMA technology proved useful in documenting functional proteomics data with the morphologic distribution of GroEL, GroES, GspD, Ndk and Pyk within formalin-fixed, paraffin-embedded cell pellets and tissues from patients with severe coronary atherosclerosis. The antibodies GroEL and GroES, which were upregulated under persistence in proteomic analysis, displayed positive reaction in atheromatous heart tissue from 10 out of 12 patients. These may be useful markers for the detection of persistent infection in vitro and in vivo.

Image-guided core-needle biopsy of peripheral lymph nodes allows the diagnosis of lymphomas

It is commonly admitted that the diagnosis of lymphomas can be assessed by the image-guided needle biopsy (IGNB) of deep lymph nodes. However, when peripheral lymph nodes are present, surgical dissection remains the standard strategy. The aim of this study was to evaluate the diagnostic yield of IGNB of peripheral lymph nodes in patients with suspected lymphomas. The records of 180 multisampling IGNBs of peripheral lymph nodes in 180 patients were reviewed. One hundred and twenty-three IGNBs were observed at first diagnosis and 57 at progression using large-cutting core-biopsy needles ranging between 18 G and 14 G in size. Immunohistochemistry studies were performed in all cases and at least one biopsy was systematically frozen. A diagnosis of lymphoma with sufficient information such that a therapeutic decision could be made was obtained in 146 of the 152 patients with lymphoproliferative disorders (96%). IGNB was equally effective in making the correct diagnosis of lymphoma at the time of original diagnosis than at relapse. The results did not depend on the biopsy site, lymph nodes size, or needle type. We recommend that IGNB may be performed as an initial procedure for the diagnosis of lymphomas either in the presence of peripheral or deep lymph nodes, as it avoids surgery.

TMA for all: a new method for the construction of tissue microarrays without recipient paraffin block using custom-built needles

BACKGROUND

TMAs are becoming a useful tool for research and quality control methods, mostly for immunohistochemistry and in situ hybridization.

METHODS

A new technique that allows building TMA blocks with more than 300 tissue cores without using a recipient paraffin block for the tissue cores and without using a commercial TMA builder instrument is described. This technique is based on the construction of TMA needles modifying conventional hypodermic needles to punch tissue cores from donor blocks, which are attached by double-side adhesive tape on a computer-generated paper grid used to align the cores on the block mould, which is filled with liquid paraffin.

RESULTS

More than two hundred TMA blocks were constructed using this method, utilized in immunohistochemistry and histochemistry as positive and negative controls and also in research.

CONCLUSION

This technique has the following advantages: it is easy to reproduce, affordable, quick and creates uniform blocks with more than 300 cores aligned, adherent and easy to cut, with negligible losses during cutting and immunohistochemistry and in situ hybridization procedures.

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.

Immunoprofiles of 11 biomarkers using tissue microarrays identify prognostic subgroups in colorectal cancer

BACKGROUND AND AIMS

Genomewide expression profiling has identified a number of genes expressed at higher levels in colorectal cancer (CRC) than in normal tissues. Our objectives in this study were: 1) to test whether genes were also distinct on the protein level; 2) to evaluate these biomarkers in a series of well-characterized CRCs; and 3) to apply hierarchical cluster analysis to the immunohistochemical data.

METHODS

Tissue microarrays (TMAs) comprising 351 CRC specimens from 270 patients were constructed to evaluate the genes Adam10, Cyclin D1, Annexin II, NFKB, Casein kinase 2 beta (CK2B), YB-1, P32, Rad51, c-fos, IGFBP4, and Connexin26 (Cx26). In total, 3,797 samples were analyzed.

RESULTS

Unsupervised hierarchical clustering discovered subgroups of CRC that differed by tumor stage and survival. Kaplan-Meier analysis showed that reduced Cx26 expression was significantly associated with shorter patient survival and higher tumor grade (G1/G2 vs G3, P = .02), and Adam10 expression with a higher tumor stage (pT1/2 vs pT3/4, P = .04).

CONCLUSIONS

Our study highlights the potential of TMAs for a higher-dimensional analysis by evaluating serial sections of the same tissue core (three-dimensional TMA analysis). In addition, it endorses the use of immunohistochemistry supplemented by hierarchical clustering for the identification of tumor subgroups with diagnostic and prognostic signatures.

Expression of tumor suppressor and tumor-related proteins in differentiated carcinoma, undifferentiated carcinoma with tubular component and pure undifferentiated carcinoma of the stomach

BACKGROUND

The recent development of tissue microarray (TMA) technology allows high-throughput protein expression profiling of cancer tissues by immunohistochemistry. We attempted to clarify the derivation of undifferentiated-type gastric carcinoma with tubular component by using TMA.

METHODS

We constructed a TMA system composed of six paraffin blocks in which 274 samples of formalin-fixed gastric carcinoma tissue from 274 patients were embedded. Using this system, we performed immunohistochemical stains for five tumor suppressor and tumor-related proteins, i.e. p53, p16, hMLH1, c-erbB-2 and carcinoembryonic antigen (CEA). The 274 gastric carcinomas were histopathologically divided into the following three groups according to the degree of differentiation: differentiated-type (D-type), undifferentiated-type with tubular component (UT-type) and pure undifferentiated-type (UP-type). Immunohistochemical results were then compared with histological types.

RESULTS

The percentages of abnormal expression of each protein in D-type, UT-type and UP-type carcinomas were as follows: 27% (38/143), 17% (17/98) and 15% (5/33) for p53; 27% (39/143), 19% (19/98) and 18% (6/33) for p16; 38% (54/143), 44% (43/98) and 24% (8/33) for hMLH1; 15% (22/143), 5% (5/98) and 0% (0/33) for c-erbB-2; and 22% (31/143), 35% (34/98) and 70% (23/33) for CEA. UP-type carcinomas exhibited the lowest frequencies of abnormal expression for p53, p16, hMLH1 and c-erbB-2, but the highest frequencies for CEA. UT-type carcinomas generally showed intermediate frequencies between those of D-type and UP-type carcinomas. Differences between D-type and UP-type for c-erbB-2 (P < 0.05) and CEA (P < 0.001) were significant, as were differences between D-type and UT-type for c-erbB-2 (P < 0.05) and CEA (P < 0.05), and differences between UT-type and UP-type for hMLH1 (P < 0.05) and CEA (P < 0.001).

CONCLUSIONS

These findings reveal that gastric carcinomas have distinct expression profiles for tumor suppressor and tumor-related proteins depending on histological types, and support the hypothesis that UT-type carcinomas are derived not only from D-type but also from UP-type carcinomas. We also found significant differences between abnormal protein expression and other clinicopathological parameters such as gender, age and status of tumor and nodes.

Technology insight: Identification of biomarkers with tissue microarray technology

High-throughput technologies have been developed in the hope of increasing the pace of biomedical research, and accelerating the rate of translation from bench to bedside. Using such technology in target discovery has resulted in the need for systematic validation of the targets in an equally rapid manner. For example, gene expression microarrays have highlighted many potential targets in cancer, and tissue microarrays have emerged as a powerful tool to validate these targets by measuring tumor-specific protein expression and linking it to clinical outcome. Automated quantitative analysis of the tissue microarray 'spots' is beginning to take the technology a step further, removing observer bias, and providing standards for quality control and the potential for high-throughput analysis. The validation required for translation of tissue biomarkers from the research lab to the clinical lab will probably rely heavily on the combination of tissue microarray technology with automated quantitative analysis.