Amplification of tissue by construction of tissue microarrays

Fetal growth at term and placental oxidative stress in a tissue micro-array model: a histological and immunohistochemistry study

This study examines 8-hydroxyguanine (8-oxo-Gua) staining in placental tissue samples based on fetal size at birth as well as its relationships with placental histology and other pregnancy variables. This prospective cohort study included women > 18 years with a singleton pregnancy, a live fetus, fluency in Italian, and delivery at term. A total of 165 pregnancies were included in the study. The nuclear syncytiotrophoblast 8-oxo-Gua staining score in LGA was substantially greater than in late FGR (p < 0.05), although the cytoplasm score was lower in SGA and LGA than in AGA (p < 0.05). Furthermore, a sex-specific pattern of 8-oxo-Gua staining was discovered in single-term placentas, with more oxidative damage found in the nuclei of syncytiotrophoblast cells and stromal and endothelial cells in AGA males compared to AGA females (p < 0.05). Second, the histological pattern of late FGR placentae differed by gender. Finally, a significant correlation (p < 0.05) was found between high-intensity 8-oxo-Gua staining in the cytoplasm of syncytiotrophoblast cells and thrombi in the chorionic plate or villi in males. On the other hand, female fetuses demonstrated a significant connection (p < 0.05) between high-intensity 8-oxo-Gua staining in endothelial and stromal cells and high birthweight MoM values. Our findings indicated a significant variation in the oxidative stress pattern between male and female placentae, implying that fetal growth is regulated differently in the two sexes.

Novel resin tissue array system reduces sample preparation time, labour and reagent costs in bone tissue histology

Resin histology plays an essential role in the analysis of hard tissues, such as bone and teeth, as well as in the context of metallic implant analysis. However, the techniques of resin embedding, followed by ground sectioning, are very costly due to significantly increased reagent cost and labour time when compared to the conventional paraffin histology approach. In the present study, a novel resin array system was developed to increase the affordability of a project analysing rat femur tissues containing metallic or polymeric implants. The resin array system enabled the simultaneous embedding of the femur samples in groups of eight samples compared to the conventional resin method where samples are processed individually. The ground sections produced with the resin array system allowed uniform ROI selection, ground section thickness, staining consistency, and histological analysis with Goldner's trichrome stain, offering a substantial opportunity for reproducible immunohistochemistry which is unable to be achieved when processing samples embedded individually. The application of this novel resin array system significantly reduced resource usage when compared to doing the same analysis on individual samples. A reduction of approximately 40% was achieved for both total labour time and total reagent cost through the use of the array system compared with individual embedding. This novel resin array system has widespread applicability to many bone, hard tissue, and metallic implant studies, offering substantial conservation of research funds and increased accessibility to advanced techniques for commercial partners due to more cost-effective sample preparation and more accurate, reproducible data.

Molecular subtyping of cancer: current status and moving toward clinical applications

Cancer is a collection of genetic diseases, with large phenotypic differences and genetic heterogeneity between different types of cancers and even within the same cancer type. Recent advances in genome-wide profiling provide an opportunity to investigate global molecular changes during the development and progression of cancer. Meanwhile, numerous statistical and machine learning algorithms have been designed for the processing and interpretation of high-throughput molecular data. Molecular subtyping studies have allowed the allocation of cancer into homogeneous groups that are considered to harbor similar molecular and clinical characteristics. Furthermore, this has helped researchers to identify both actionable targets for drug design as well as biomarkers for response prediction. In this review, we introduce five frequently applied techniques for generating molecular data, which are microarray, RNA sequencing, quantitative polymerase chain reaction, NanoString and tissue microarray. Commonly used molecular data for cancer subtyping and clinical applications are discussed. Next, we summarize a workflow for molecular subtyping of cancer, including data preprocessing, cluster analysis, supervised classification and subtype characterizations. Finally, we identify and describe four major challenges in the molecular subtyping of cancer that may preclude clinical implementation. We suggest that standardized methods should be established to help identify intrinsic subgroup signatures and build robust classifiers that pave the way toward stratified treatment of cancer patients.

Recommendations for Tissue Microarray Construction and Quality Assurance

Tissue microarrays (TMAs) are important tools to conserve precious tissue resources from increasingly smaller biopsies and to control experimental costs and variation across sample sets. The quality assurance assessment of TMA materials created at centralized biobanks has not been standardized. Herein, we outline 2 processes for the construction of TMAs ("recipient block" and "tape" methods) and the associated preconstruction quality control measures (pathology review, protein and RNA assessment, map creation, and storage conditions) developed by the AIDS Cancer Specimen Resource (ACSR) Network's Science and Technology Core. These steps provide a suggested framework for quality assessment that allows end-users, receiving materials from tissue banks, confidence in their experimental results.

HER2 Amplification Status in Feline Mammary Carcinoma: A Tissue Microarray-Fluorescence In Situ Hydridization-Based Study

Human epidermal growth factor receptor 2 (HER2) is a tyrosine kinase receptor overexpressed in a subset of breast cancer due to HER2 gene amplification. HER2 protein is expressed in feline mammary carcinomas, but little is known about its cytogenetic alterations. The aim of this study was to evaluate HER2 gene amplification status and its correlation with HER2 protein expression in feline mammary carcinomas. Feline mammary carcinomas were retrospectively selected and immunohistochemically (IHC) evaluated for HER2 protein expression. All the HER2 IHC-positive (3+) and equivocal (2+) cases and a subset of negative cases (0/1+) were selected for fluorescence in situ hybridization (FISH). Dual-core tissue microarrays were prepared for FISH. IHC and FISH were evaluated according to the 2013 American Society of Clinical Oncology/College of American Pathologists guidelines. The study included 107 feline mammary carcinomas from 88 queens. HER2 protein expression was positive (3+) in 7 cases (6.5%), equivocal (2+) in 48 cases (45%), and negative (0/1+) in 52 cases (48.5%). HER2 status was indeterminate in 8 feline mammary carcinomas (12%), amplified in 3 (4%), equivocal in 4 (6%), and nonamplified in 53 (78%). HER2 gene amplification and protein expression were significantly positively correlated ( R = 0.283; P < .0001). HER2 gene is amplified in a subset of feline mammary carcinomas despite the HER2 positive or equivocal protein expression, but it remains to be determined if the HER2 amplification is a gene alteration that drives mammary tumor carcinogenesis or only a bystander passenger mutation.

Anti-Inflammatory Drug Use and Ovarian Cancer Risk by COX1/COX2 Expression and Infiltration of Tumor-Associated Macrophages

BACKGROUND

Nonsteroidal anti-inflammatory drug (NSAID) use may affect ovarian cancer risk via prostaglandin synthesis and tumor-associated macrophage (TAM) infiltration. We evaluated if associations between aspirin or non-aspirin NSAID use and ovarian cancer risk differed by tumor expression of prostaglandin-related (COX1, COX2) and TAM-related (CD68, CD163) markers.

METHODS

We evaluated cases and matched controls from the Nurses' Health Study (NHS), NHSII, and New England Case-Control Study (NECC). Cases with IHC data on COX1 and COX2 (n = 532) or CD68 and CD163 (n = 530) were included. We used polytomous logistic regression, adjusted for ovarian cancer risk factors, to estimate OR for NSAID use and ovarian cancer risk by marker level.

RESULTS

Recent aspirin use had a nonsignificant inverse association and recent non-aspirin NSAID use had no association with ovarian cancer risk. NSAID use was not differentially associated with ovarian cancer by COX1 or COX2 expression. However, recent aspirin use was associated with lower ovarian cancer risk for high [OR 0.54; 95% confidence interval (CI), 0.37-0.78], but not low (OR 1.50; 95% CI, 0.97-2.31), CD163 density (P _{heterogeneity} < 0.001). Similar results were observed for aspirin duration and tablets and for recent non-aspirin NSAID use. Results were not clearly different by macrophage density defined by the less specific macrophage marker, CD68.

CONCLUSIONS

NSAID use was inversely associated with risk of ovarian cancer with high density CD163, a marker for M2-type, immunosuppressive macrophages. However, the relationship did not differ by prostaglandin synthesis markers.

IMPACT

Future research should explore prostaglandin-independent mechanisms for the association between NSAID use and ovarian cancer risk, including immune mechanisms.

CDK9 Expression Shows Role as a Potential Prognostic Biomarker in Breast Cancer Patients Who Fail to Achieve Pathologic Complete Response after Neoadjuvant Chemotherapy

Failure to achieve pathologic complete response is associated with poor prognosis in breast cancer patients following neoadjuvant chemotherapy (NACT). However, prognostic biomarkers for clinical outcome are unclear in this patient population. Cyclin-dependent kinase 9 (CDK9) is often dysregulated in breast cancer, and its deficiency results in genomic instability. We reviewed the records of 84 breast cancer patients from Emory University's Winship Cancer Institute who had undergone surgical resection after NACT and had tissue available for tissue microarray analysis (TMA). Data recorded included disease presentation, treatment, pathologic response, overall survival (OS), locoregional recurrence free survival (LRRFS), distant-failure free survival (DFFS), recurrence-free survival (RFS), and event-free survival (EFS). Immunohistochemistry was performed on patient samples to determine CDK9 expression levels after NACT. Protein expression was linked with clinical data to determine significance. In a Cox proportional hazards model, using a time-dependent covariate to evaluate the risk of death between groups beyond 3 years, high CDK9 expression was significantly associated with an increase in OS (HR: 0.26, 95% CI: 0.07-0.98, p=0.046). However, Kaplan-Meier curves for OS, LRRFS, DFFS, RFS, and EFS did not reach statistical significance. The results of this study indicate that CDK9 may have a potential role as a prognostic biomarker in patients with breast cancer following NACT. However, further validation studies with increased sample sizes are needed to help elucidate the prognostic role for CDK9 in the management of these patients.

JMJD1A, H3K9me1, H3K9me2 and ADM expression as prognostic markers in oral and oropharyngeal squamous cell carcinoma

Aims

Jumonji Domain-Containing 1A (JMJD1A) protein promotes demethylation of histones, especially at lysin-9 of di-methylated histone H3 (H3K9me2) or mono-methylated (H3K9me1). Increased levels of H3 histone methylation at lysin-9 (H3K9) is related to tumor suppressor gene silencing. JMJD1A gene target Adrenomeduline (ADM) has shown to promote cell growth and tumorigenesis. JMJD1A and ADM expression, as well as H3K9 methylation level have been related with development risk and prognosis of several tumor types.

Methods and results

We aimed to evaluate JMJD1A, ADM, H3K9me1 and H3K9me2expression in paraffin-embedded tissue microarrays from 84 oral and oropharyngeal squamous cell carcinoma samples through immunohistochemistry analysis. Our results showed that nuclear JMJD1A expression was related to lymph node metastasis risk. In addition, JMJD1A cytoplasmic expression was an independent risk marker for advanced tumor stages. H3K9me1 cytoplasmic expression was associated with reduced disease-specific death risk. Furthermore, high H3K9me2 nuclear expression was associated with worse specific-disease and disease-free survival. Finally, high ADM cytoplasmic expression was an independent marker of lymph node metastasis risk.

Conclusion

JMJD1A, H3K9me1/2 and ADM expression may be predictor markers of progression and prognosis in oral and oropharynx cancer patients, as well as putative therapeutic targets.

Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks

Cellular heterogeneity poses a substantial challenge to understanding tissue-level phenotypes and confounds conventional bulk analyses. To analyze signaling at the single-cell level in human tissues, we applied mass cytometry using cytometry time of flight to formalin-fixed, paraffin-embedded (FFPE) normal and diseased intestinal specimens. This technique, called FFPE-DISSECT (disaggregation for intracellular signaling in single epithelial cells from tissue), is a single-cell approach to characterizing signaling states in embedded tissue samples. We applied FFPE-DISSECT coupled to mass cytometry and found differential signaling by tumor necrosis factor-α in intestinal enterocytes, goblet cells, and enteroendocrine cells, implicating the downstream RAS-RAF-MEK pathway in determining goblet cell identity. Application of this technique and computational analyses to human colon specimens confirmed the reduced differentiation in colorectal cancer (CRC) compared to normal colon and revealed increased intratissue and intertissue heterogeneity in CRC with quantitative changes in the regulation of signaling pathways. Specifically, coregulation of the kinases p38 and ERK, the translation regulator 4EBP1, and the transcription factor CREB in proliferating normal colon cells was lost in CRC. Our data suggest that this single-cell approach, applied in conjunction with genomic annotation, enables the rapid and detailed characterization of cellular heterogeneity from clinical repositories of embedded human tissues. This technique can be used to derive cellular landscapes from archived patient samples (beyond CRC) and as a high-resolution tool for disease characterization and subtyping.

β-Defensin-2 is overexpressed in human vocal cord polyps

The objective of the study is to investigate the expression of human β-defensin-1 (hBD-1) and human β-defensin-2 (hBD-2) in vocal cord polyps using tissue microarray. Tissue specimens from vocal cord polyps (N = 51), vocal cord nodules (N = 26), and healthy vocal cords (N = 8) were retrieved from the biobank of the Department of Pathology of Tianjin Tianhe Hospital between 2003 and 2006 and immunostained on tissue microarrays for the quantitative analysis of hBD-1 and hBD-2 expression. hBD-1 expression did not differ significantly between healthy vocal cords, vocal cord nodules, and vocal cord polyps (p = 0.904). In contrast, hBD-2 expression was significantly higher in vocal cord polyps compared to vocal cord nodules and healthy vocal cords (p < 0.001). The expression of hBD-2, but not hBD-1, is elevated in vocal cord polyp epithelium. This suggests that hBD-1 has a more constitutive role in host defense in the vocal cords, whereas hBD-2 expression may be a result of local inflammation or the presence of invading pathogens.

Living Cell Microarrays: An Overview of Concepts

Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays.

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

Immunohistochemistry is a commonly used clinical and research lab detection technique for investigating protein expression and localization within tissues. Many semi-quantitative systems have been developed for scoring expression using immunohistochemistry, but inherent subjectivity limits reproducibility and accuracy of results. Furthermore, the investigation of spatially overlapping biomarkers such as nuclear transcription factors is difficult with current immunohistochemistry techniques. We have developed and optimized a system for simultaneous investigation of multiple proteins using high throughput methods of multiplexed immunohistochemistry and multispectral imaging. Multiplexed immunohistochemistry is performed by sequential application of primary antibodies with secondary antibodies conjugated to horseradish peroxidase or alkaline phosphatase. Different chromogens are used to detect each protein of interest. Stained slides are loaded into an automated slide scanner and a protocol is created for automated image acquisition. A spectral library is created by staining a set of slides with a single chromogen on each. A subset of representative stained images are imported into multispectral imaging software and an algorithm for distinguishing tissue type is created by defining tissue compartments on images. Subcellular compartments are segmented by using hematoxylin counterstain and adjusting the intrinsic algorithm. Thresholding is applied to determine positivity and protein co-localization. The final algorithm is then applied to the entire set of tissues. Resulting data allows the user to evaluate protein expression based on tissue type (ex. epithelia vs. stroma) and subcellular compartment (nucleus vs. cytoplasm vs. plasma membrane). Co-localization analysis allows for investigation of double-positive, double-negative, and single-positive cell types. Combining multispectral imaging with multiplexed immunohistochemistry and automated image acquisition is an objective, high-throughput method for investigation of biomarkers within tissues.

Development of living cell microarrays using non-contact micropipette printing

During the last 30 years cellular screening systems were unidirectional developed towards high throughput applications on single cell level. We developed living cell microarrays, which provide an in vivo-like microenvironment for an advanced method to measure cellular response to external stimuli. To print living cells on glass slides, the classic microarray equipment, which involves printer and scanner, was fully transferred to suspensions of living cells. The microarray production was optimized using a contact-free spotting procedure in order to enhanced cell adhesion and growth rates. The printed model cells, A-549 (lung cancer cell line), were analyzed with conventional cell staining assays like DAPI (cell nuclei staining), calcein acetoxymethyl ester (viable cell staining), and CellTiter-Blue(®) Cell Viability Assay. After optimization, a reproducible (spot-to-spot variation: ± 8.6 cells) printing method for small living cell amounts (1200 cells and fewer) was established that achieved cell viabilities of up to 88% for ≥ 0.6 μL and good proliferation characteristics. Hence, this method could be advantageous for use in biomedical and diagnostic applications.

Comparison of immunohistochemistry and mRNA in situ hybridization in detecting thyroid transcription factor-1 expression in non-small cell lung carcinomas tissue

Thyroid transcription factor-1 (TTF-1) reportedly possesses oncogenic and suppressive roles within the same tumor type and may play a dual function in the progression of lung cancer. Immunohistochemistry (IHC) and mRNA in situ hybridization (ISH) are commonly used methods for detecting protein or mRNA expression. The present study compared the concordance rate of the two methods in the evaluation of thyroid transcription factor-1 (TTF-1) expression in non-small cell lung carcinoma (NSCLC) using tissue microarray-based IHC and mRNA ISH. TTF-1 protein and mRNA expression levels were examined in 196 cases of NSCLC. The IHC and mRNA ISH agreement was 91.3% (179/196), and near-perfect agreement was observed between the two methods (κ-coefficient, 0.848). There was no significant difference between IHC and mRNA ISH, as analyzed by the McNemar-Bowker test (P=0.219). The present findings proved that IHC is comparable to mRNA ISH for evaluating TTF-1 expression in NSCLC. These two methods can be used to detect TTF-1 expression in future studies.

Integrin αvβ6 sustains and promotes tumor invasive growth in colon cancer progression

AIM: To detect the mechanism by which colon tumor escapes the growth constraints imposed on normal cells by cell crowding and dense pericellular matrices.

METHODS: An immunohistochemical study of integrin αvβ6 and matrix metalloproteinase-9 (MMP-9) was performed on tissue microarrays of 200 spots, including 100 cases of colon tumors.

RESULTS: High immunoreactivity for αvβ6 (73.7%; 28/38) and MMP-9 (76.5%; 52/68) was observed in invasive tumor portions. Furthermore, the effects of integrin αvβ6 on tumor invasive growth in nude mice were detected. Tumor invasive growth and high expression of both αvβ6 and MMP-9 were only seen in tumors resulting from WiDr cells expressing αvβ6 in the tumorigenicity assay. Flow cytometry was applied to analyze αvβ6 expression in colon cancer WiDr and SW480 cells. The effects of cell density on αvβ6 expression and MMP-9 secretion were also detected by Biotrak MMP-9 activity assay and gelatin zymography assay. High cell density evidently enhanced αvβ6 expression and promoted MMP-9 secretion compared with low density.

CONCLUSION: Integrin αvβ6 sustains and promotes tumor invasive growth in tumor progression via a self-perpetuating mechanism. Integrin ανβ6-mediated MMP-9 secretion facilitates pericellular matrix degradation at high cell density, which provides the basis of invasive growth.

Tissue microarray technology and findings for diagnostic immunohistochemistry

AIMS

This study was undertaken to determine the validity and viability of tissue microarray (TMA) technology in assessing diagnostic immunohistochemistry (IHC) at a single laboratory site.

METHODS

IHC using 57 primary antibodies was performed on a TMA paraffin block containing 89 cores of duplicate previously identified 1 mm diameter tissue specimens. IHC was interpreted by a histology scientist with IHC experience, with pathologist assistance if required. Review of the literature was performed to investigate cases of unexpected immunoreactivity.

RESULTS

55 of 57 antibodies had expected positive staining against the TMA tissue panel that correlated with the original paraffin blocks. Immunostaining of duplicate 1 mm cores correlated with the originally sourced paraffin block in 42 of 43 (98%) tissue types. Some antibodies had unexpected positive immunoreactivity.

DISCUSSION

TMA technology can be utilised effectively in the diagnostic IHC laboratory as a universal positive multiple tissue control block for routine IHC, and can provide valuable information for the benefit of histology scientists and pathologists with respect to interpretation of IHC staining.

Markers of epithelial to mesenchymal transition in association with survival in head and neck squamous cell carcinoma (HNSCC)

BACKGROUND

Elucidating the molecular phenotype of cancers with high metastatic potential will facilitate the development of novel therapeutic approaches to the disease. Gene expression profiles link epithelial to mesenchymal transition (EMT) phenotype with high-risk HNSCC. We sought to determine the role of protein biomarkers of EMT in head and neck squamous carcinoma (HNSC) prognosis.

METHODS

Protein expression analysis of EGFR, β-catenin and E-cadherin was performed on a cohort of 102 patients with HNSCC recruited between 1992 and 2005 using automated quantitative protein analysis (AQUA). We evaluated associations with clinicopathological parameters and prognosis.

RESULTS

There were 67 patients with primary squamous cell carcinoma of the head and neck in this cohort who met inclusion criteria and for whom we had complete E-cadherin, beta-catenin and EGFR expression data. High E-cadherin expressers had longer 5-year progression-free survival (PFS) compared to those with low E-cadherin (59.7% versus 40.6%, p = 0.04) and overall survival (OS) (69.6% versus 44.3%, p  = 0.05). Kaplan-Meier analysis showed that patients with low beta-catenin-expressing tumors trended toward worse 5-year PFS (p = 0.057). High EGFR expressers had inferior OS compared to low EGFR expressers (27.7% vs. 54%, p = 0.029). In the multivariable analysis context, E-cadherin remained an independent predictor of improved OS (HR = 0.204, 95% CI 0.043 to 0.972, p = 0.046) while EGFR trended towards significance for OS.

CONCLUSIONS

The putative markers of EMT defined within a panel of HNSCC using AQUA are associated with tumors of poor prognosis.

Macrophage expression of tartrate-resistant acid phosphatase as a prognostic indicator in colon cancer

Recent research has indicated that separate populations of macrophages are associated with differing outcomes in cancer survival. In our study, we examine macrophage expression of tartrate-resistant acid phosphatase (TRAP) and its effect on survival in colon cancer. Immunohistochemical analysis on colorectal adenocarcinomas confirmed macrophage expression of TRAP. Co-localization of TRAP with CD68, a pan-macrophage marker, revealed that TRAP is present in some but not all sub-populations of macrophages. Further co-localization of TRAP with CD163, an M2 marker, revealed that TRAP is expressed by both M2 and non-M2 macrophages. TRAP expression was then measured using the AQUA method of quantitative immunofluorescence in a tissue microarray consisting of 233 colorectal cancer patients seen at Yale-New Haven Hospital. Survival analysis revealed that patients with high TRAP expression have a 22 % increase in 5-year survival (uncorrected log-rank p = 0.025) and a 47 % risk reduction in disease-specific death (p = 0.02). This finding was validated in a second cohort of older cases consisting of 505 colorectal cancer patients. Patients with high TRAP expression in the validation set had a 19 % increase in 5-year survival (log-rank p = 0.0041) and a 52 % risk reduction in death (p = 0.0019). These results provide evidence that macrophage expression of TRAP is associated with improved outcome and implicates TRAP as a potential biomarker in colon cancer.

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.

Construction and analysis of multiparameter prognostic models for melanoma outcome

The outcome of Stage II melanoma is uncertain. Despite that 10-year melanoma-specific survival can approach 50 % following curative-intent wide local excision and negative sentinel lymph node biopsy, the adverse risk-benefit ratio of interferon-based adjuvant regimens precludes their use in most patients. The discovery and translation of protein-based prognostic biomarkers into the clinic offers the promise for residual risk stratification of Stage II melanoma patients beyond conventional clinicopathologic criteria to identify an additional subset of patients who, based upon tumor molecular profiles, might also derive benefit from adjuvant regimens. Despite incorporation of Ki-67 assays into clinical practice, systematic review of REMARK-compliant, immunostain-based prognostic biomarker assays in melanoma suggests that residual risk of recurrence might be best explained by a composite score derived from a small panel of proteins representing independent features of melanoma biology. Reflecting this trend, to date, five such multiparameter melanoma prognostic models have been published. Here, we review these five models and provide detailed protocols for discovering and validating multiparameter models including: appropriate cohort recruitment strategies, comprehensive laboratory protocols supporting fully quantitative chromogenic or fluorescent immunostaining platforms, statistical approaches to create composite prognostic indices recommended steps for model validation in independent cohorts.

Alterations of C-MYC, NKX3.1, and E-cadherin expression in canine prostate carcinogenesis

The dog (canis lupus familiaris) is the only other species besides humans that develop spontaneous prostatic carcinomas (PCa) at a high frequency. The canine model is primarily utilized for the study of the PCa molecular mechanisms and provides a natural animal model for the study of potential therapies. In humans, the PCa frequently exhibits mutations in the C-MYC and a reduced expression of the E-cadherin and NKX3.1 proteins. This study's objective was to evaluate the NKX3.1, C-MYC, and E-cadherin expression in the canine normal prostate, benign prostatic hyperplasia (BPH), proliferative inflammatory atrophy (PIA) and PCa and to verify differences in expression and subcellular localization of these proteins in the prostatic carcinogenesis. A tissue microarray (TMA) slide was constructed, and immunohistochemistry with antibodies raised against C-MYC, NKX3.1, E-cadherin and p63 was performed using the peroxidase and DAB methods. The C-MYC protein expression was elevated in the cytoplasm and nuclei of the canine PCa and PIA compared with the normal prostate (P = 0.004. The NKX3.1 protein expression was reduced in 94.75% of the PCa and 100% of the PIA compared with the normal prostate (P = 0.0022). In fact, the expression of E-cadherin trended towards a decrease in carcinomas when compared to normal prostate and PIA. By immunohistochemistry, more p63-positive basal cells were observed in the PCa and PIA when compared with the normal prostate (P = 0.0002). This study has demonstrated that the carcinogenesis of canine prostatic tissue may be related to basal cell proliferation, the gain of C-MYC function and the loss of NKX3.1 protein expression.

The cell block technique revisited for cells cultured in adherence and as "spheres"

A simple modification of the cell block technique for cultured cells grown in different conditions and suitable for the construction of tissue micro arrays (TMA) is described. The application of mechanical stirring during clot formation allows the uniform dispersion of cells in the fibrin mesh, thus increasing the final volume of the embedded material of evenly distributed cells. This technique is easily applied to spheres-obtained from cell lines cultured under appropriate conditions-that are enriched in stem cells. The possibility of constructing TMA using cell lines (grown in adherence and as spheres) and samples of the corresponding tumors or normal tissues may allow the direct comparison of original tumors with in vitro-expanded cell lines.

FAS/FASL expression profile as a prognostic marker in squamous cell carcinoma of the oral cavity

FAS/FASL altered expression may cause tumor protecting immunomodulation, with a direct impact on patient prognosis. FAS expression was studied in 60 squamous cell carcinomas of the oral cavity. FAS expression did not show a significant association with tumor histopathological characteristics, but was significantly associated with lymph node positivity. FAS expression was significantly associated with disease specific death and negative FAS expression was an independent risk factor, increasing risk 4 times when compared to positive expression. When FAS and FASL expression results were combined, we were able to define high, intermediate and low risk profiles. Disease-free and disease-specific survival were significantly correlated with FAS/FASL expression profiles. The high risk category was an independent marker for earlier disease relapse and disease-specific death, with approximately 4- and 6-fold increased risk, respectively, when compared to the low risk profile. Risk profiles based on FAS/FASL expression showed that high risk was significantly associated with increased disease relapse and death, as well as shorter disease-free or disease-specific survival. This categorization, added to patient clinical data, may facilitate the choice of therapy, minimizing treatment failure and increasing disease control.

Tissue microarrays: leaping the gap between research and clinical adoption

The use of tissue microarrays (TMAs) in the preclinical and translational research settings has become ubiquitous as they allow for high-throughput in situ biomarker analysis of hundreds of patient samples, with time and cost efficiency. Coupled with advanced imaging and image-analysis technologies that allow for objective and standardized biomarker expression assessment, TMAs have become critical tools for the development and validation of clinically meaningful biomarker diagnostic assays. However, their diagnostic use in the clinical laboratory setting is limited due to the need for conventional whole-section tissue assessment used for routine diagnostic purposes. In this article, after reviewing TMA basics and their translational and clinical research applications, we will focus on the use of TMAs for robust assay development and quality control in the clinical laboratory setting, as well as provide insights into how TMAs may serve well in the clinical setting as assay performance and quantification controls.

Expression of girdin in human colorectal cancer and its association with tumor progression

BACKGROUND

Girdin is crucial for cellular motility in cancer cell lines and for metastasis in a mouse model. Its expression has been demonstrated in a range of cancers by a few studies and was a prognostic factor in a subset of patients.

OBJECTIVE

The aim of this study was to investigate the relationship of Girdin expression to clinicopathologic factors in terms of the progression of colorectal cancers and patient survival.

DESIGN

This study is a retrospective review of immunohistochemical and clinicopathologic data.

SETTING

This study was conducted at a tertiary care hospital/referral center in South Korea.

PATIENTS

Tissue microarrays were made from surgical biopsies of 298 patients with colorectal cancer diagnosed between November 1996 and August 2007. Patients were included in the study if their survival time was known and if well-preserved surgical biopsy specimens were available.

MAIN OUTCOME MEASURES

The primary outcomes measured were Girdin expression and its association in tumor progression and patient survival.

RESULTS

Positive staining for Girdin was observed in samples from 66 of 242 patients (27.3%). Expression of Girdin was significantly associated with tumor-node-metastasis stage (p = 0.036), liver metastasis (p = 0.025), and metastases involving the liver and other organs (p = 0.009). However, Girdin expression did not correlate significantly with the overall survival of patients and was not a significant negative prognostic factor for survival by univariate or multivariate analyses.

LIMITATIONS

The number of investigated patients and the number of cases with positive staining for Girdin were rather small for the multivariate analysis. The inclusion time frame is long and includes other surgical and medical improvements, which influence a patient's survival.

CONCLUSION

The expression of Girdin is related to tumor metastasis but not to survival in human colorectal cancers.

FGFR4 profile as a prognostic marker in squamous cell carcinoma of the mouth and oropharynx

Background

Fibroblast growth factor receptor 4 (FGFR4) is a member of a receptor tyrosine kinase family of enzymes involved in cell cycle control and proliferation. A common single nucleotide polymorphism (SNP) Gly388Arg variant has been associated with increased tumor cell motility and progression of breast cancer, head and neck cancer and soft tissue sarcomas. The present study evaluated the prognostic significance of FGFR4 in oral and oropharynx carcinomas, finding an association of FGFR4 expression and Gly388Arg genotype with tumor onset and prognosis.

Patients and Methods

DNA from peripheral blood of 122 patients with oral and oropharyngeal squamous cell carcinomas was used to determine FGFR4 genotype by PCR-RFLP. Protein expression was assessed by immunohistochemistry (IHC) on paraffin-embedded tissue microarrays.

Results

Presence of allele Arg388 was associated with lymphatic embolization and with disease related premature death. In addition, FGFR4 low expression was related with lymph node positivity and premature relapse of disease, as well as disease related death.

Conclusion

Our results propose FGFR4 profile, measured by the Gly388Arg genotype and expression, as a novel marker of prognosis in squamous cell carcinoma of the mouth and oropharynx.

Evaluation of HER2 gene amplification in breast cancer using nuclei microarray in situ hybridization

Fluorescence in situ hybridization (FISH) assay is considered the “gold standard” in evaluating HER2/neu (HER2) gene status. However, FISH detection is costly and time consuming. Thus, we established nuclei microarray with extracted intact nuclei from paraffin embedded breast cancer tissues for FISH detection. The nuclei microarray FISH (NMFISH) technology serves as a useful platform for analyzing HER2 gene/chromosome 17 centromere ratio. We examined HER2 gene status in 152 cases of invasive ductal carcinomas of the breast that were resected surgically with FISH and NMFISH. HER2 gene amplification status was classified according to the guidelines of the American Society of Clinical Oncology and College of American Pathologists (ASCO/CAP). Comparison of the cut-off values for HER2/chromosome 17 centromere copy number ratio obtained by NMFISH and FISH showed that there was almost perfect agreement between the two methods (κ coefficient 0.920). The results of the two methods were almost consistent for the evaluation of HER2 gene counts. The present study proved that NMFISH is comparable with FISH for evaluating HER2 gene status. The use of nuclei microarray technology is highly efficient, time and reagent conserving and inexpensive.

The nonreceptor-type tyrosine phosphatase PTPN13 is a tumor suppressor gene in non-small cell lung cancer

The aim of the present work was to identify protein tyrosine phosphatases (PTPs) as novel, candidate tumor suppressor genes in lung cancer. Among the 38 PTPs in the human genome that show specificity for phosphotyrosine, we identified six PTPs by quantitative RT-PCR whose mRNA expression levels were significantly down-regulated in lung cancer-derived cell lines (ie, PTPRE, PTPRF, PTPRU, PTPRK, PTPRD, and PTPN13). After validation in primary samples of non-small cell lung cancer (NSCLC), we selected PTPN13 for further studies. The results presented here demonstrate that PTPN13 is a candidate tumor suppressor gene that is frequently inactivated in NSCLC through the loss of either mRNA and protein expression (64/87, 73%) or somatic mutation (approximately 8%). Loss of PTPN13 expression was apparently due to the loss of one or both copies of the PTPN13 locus at 4q (approximately 26% double deletion and approximately 37% single deletion) but not to promoter methylation. Finally, the manipulation of PTPN13 expression in lung cancer cells (ie, NCI-H292, A549) demonstrated that PTPN13 negatively regulates anchorage-dependent and anchorage-independent growth in vitro and restrains tumorigenicity in vivo, possibly through the control of the tyrosine phosphorylation of both EGFR and HER2. In conclusion, the expression screening of PTPs in lung cancer reported here has identified PTPN13 as a novel candidate tumor suppressor in NSCLC whose loss increases signaling from epidermal growth factor receptor and HER2 tyrosine kinase receptors.

Expression of the ribosomal proteins Rplp0, Rplp1, and Rplp2 in gynecologic tumors

Previous work from our laboratory has demonstrated that the expression of the ribosomal protein Rplp1 immortalizes primary cells and is involved in transformation. To investigate the role of the P proteins in tumorigenesis, we examined the messenger RNA expression levels of Rplp0, Rplp1, and Rplp2 in a series of 32 patients with gynecologic tumors. The messenger RNA expression level of all 3 P proteins was increased significantly in the tumor tissue, compared with normal tissue. In addition, a total of 140 biopsies of gynecologic cancers (46 endometrioid and 94 ovarian) were investigated. An up-regulation of P protein expression was observed by immunohistochemistry in an average of 27% of the tumors, as compared with normal tissues. Moreover, the level of P protein up-regulation correlated significantly with p53 expression in serous ovarian cancers. This is an important fact because the level of overexpression of the P proteins correlated with the presence of lymph node metastases in serous ovarian cancers. We also observed that endometrial carcinomas that had invaded the myometrium overexpressed P proteins in the invasive front. In addition, we found that the P proteins are up-regulated in a considerable number of patients with the most common types of cancer. Overall, our study shows that P proteins are involved in human cancer and indicates that the expression level of these proteins could be useful as a prognostic marker in specific subtypes of gynecologic tumors.

Oncogenic role of the E3 ubiquitin ligase NEDD4-1, a PTEN negative regulator, in non-small-cell lung carcinomas

Loss of the PTEN tumor suppressor gene occurs frequently in non-small-cell lung carcinoma (NSCLC), although neither genetic alterations nor epigenetic silencing are significant predictors of PTEN protein levels. Since recent reports implicated neural precursor cell expressed, developmentally down-regulated 4-1 (NEDD4-1) as the E3 ubiquitin ligase that regulates PTEN stability, we investigated the role of NEDD4-1 in the regulation of PTEN expression in cases of NSCLC. Our findings indicate that NEDD4-1 plays a critical role in the development of NSCLC and provides novel insight on the mechanisms that contribute to inactivate PTEN in lung cancer. Immunohistochemical analysis on tissue microarrays containing 103 NSCLC resections revealed NEDD4-1 overexpression in 80% of tumors, which correlated with the loss of PTEN protein (n=98; P<0.001). Accordingly, adoptive NEDD4-1 expression in NSCLC cells decreased PTEN protein stability, whereas knock-down of NEDD4-1 expression decreased PTEN ubiquitylation and increased PTEN protein levels. In 25% of cases, NEDD4-1 overexpression was due to gene amplification at 15q21. In addition, manipulation of NEDD4-1 expression in different lung cell systems demonstrated that suppression of NEDD4-1 expression significantly reduced proliferation of NSCLC cells in vitro and tumor growth in vivo, whereas NEDD4-1 overexpression facilitated anchorage-dependent and independent growth in vitro of nontransformed lung epithelial cells that lack pRB and TP53 (BEAS-2B). NEDD4-1 overexpression also augmented the tumorigenicity of lung cancer cells that have an intact PTEN gene (NCI-H460 cells).

Expression of protease activated receptor-2 in human colorectal cancer and its association with tumor progression

PURPOSE

Protease activated receptor-2 has been reported to promote the proliferation of colorectal cancer cells. The aim of this study was to investigate the relationship of protease activated receptor-2 expression to clinicopathologic factors to clarify its role in tumor progression and patient survival in human colorectal cancer.

METHODS

Immunohistochemical staining with anti-protease activated receptor-2 antibody was carried out and evaluated on samples from 295 patients with colorectal cancer obtained during surgical treatment at Kangnam St. Mary's Hospital, Seoul, Republic of Korea. Medical records were reviewed and relationships between immunostaining and clinicopathologic findings were evaluated.

RESULTS

Positive staining for protease activated receptor-2 was observed in samples from 100 patients (33.9%). Expression of protease activated receptor-2 was significantly associated with depth of tumor invasion (P = .013), liver metastasis (P = .008), TNM stage (P = .009), and tumor location (P = .011). However, protease activated receptor-2 expression did not significantly correlate with overall survival of patients and was not a significant negative prognostic factor for survival in univariate or multivariate analyses.

CONCLUSIONS

The expression of protease activated receptor-2 is related to tumor invasion and metastasis in human colorectal cancer. However, further studies are needed to clarify the role of protease activated receptor-2 in the prognosis of patients with colorectal cancer.

Formalin fixation and immunoreactivity in prostate cancer and benign prostatic tissues

For better fixation, formalin injection of radical prostatectomy (RP) specimens has been suggested. We aimed to assess its effect on immunoreactivity using immunohistochemistry (IHC). A tissue microarray of cancer and benign tissues from 42 RP specimens was constructed. Twenty-one of the prostates had been injected with formalin prior to formalin immersion. IHC staining was performed using 15 antibodies, including nuclear and cytoplasmic markers known to be positive in prostate tissue: pan cytokeratin, P504S, high molecular weight (HMW) keratin, PSA, vimentin, actin HHF35, thioredoxin-1, peroxiredoxin-2, PDX-1, BAX, p27, androgen receptor (AR) and heat shock proteins (HSP) 27, 60 and 70. Differences in staining intensity in cancer and benign tissues were compared separately except for HMW keratin. Only 7 of 29 analyses showed significant differences between groups, including 5 of 15 antibodies. The expression of AR and HSP 27 was stronger in formalin-injected tissue, while the opposite was true for HSP 60, HSP 70 and peroxiredoxin-2. For most antibodies, formalin injection does not significantly affect immunoreactivity in prostate tissue. The staining variability caused by inter- and intratumoral heterogeneity may be greater than that caused by the fixation method.

Quantitative evaluation of protein expression as a function of tissue microarray core diameter: is a large (1.5 mm) core better than a small (0.6 mm) core?

CONTEXT

Tissue microarrays (TMAs) have emerged as a high-throughput technology for protein evaluation in large cohorts. This technique allows maximization of tissue resources by analysis of sections from 0.6-mm to 1.5-mm core "biopsies" of standard formalin-fixed, paraffin-embedded tissue blocks and by the processing of hundreds of cases arrayed on a single recipient block in an identical manner.

OBJECTIVE

To assess the expression of a series of biomarkers as a function of core size. Although pathologists frequently feel better if larger core sizes are used, there is no evidence in the literature showing that large cores are better (or worse) than small cores for assessment of TMAs.

DESIGN

Estrogen receptor, HER2/neu, epidermal growth factor receptor, STAT3, mTOR, and phospho-p70 S6 kinase were measured by immunofluorescence with automated quantitative analysis. One random 0.6-mm field (one 0.6-mm spot) was compared to 6 to 12 fields per spot, representing 1-mm and 1.5-mm cores, for 3 different tumor types.

RESULTS

We show that measurement of a single random 0.6-mm spot was comparable to analysis of the whole 1-mm or 1.5-mm spot (Pearson R coefficient varying from 0.87-0.98) for all markers tested.

CONCLUSIONS

Since TMA technology is now being used in all phases of biomarker development, this work shows that TMAs with 0.6-mm cores are as representative as those with any common larger core size for optimization of standardized experimental conditions. Given that a greater number of 0.6-cores can be arrayed in a single master block, use of this core size allows increased throughput and decreased cost.

Intra- and interobserver reproducibility of interpretation of immunohistochemical stains of prostate cancer

The evaluation of immunohistochemistry (IHC) is usually semiquantitative, and thus subject to observer variability. We analyzed the reproducibility of different IHC measures. Fifty TMA cores of prostate cancer were stained for PDX-1, a transcription factor overexpressed in the cytoplasm of prostate cancer cells. The strongest intensity was scored 0-3 and 1-3 was used for extent (1-33%, 34-66%, and 67-100%). The stains were evaluated twice by four observers: two genitourinary pathologists, and two medical doctors with no formal pathology training. Staining intensity was also measured with automated image analysis. The pathologists read the slides faster than nonpathologists (total time 88 and 178 min, respectively, p = 0.03). Mean weighted kappa for intraobserver agreement was 0.85 (range 0.81-0.89) for intensity and 0.43 (range 0.38-0.51) for extent with similar results among pathologists and nonpathologists. Mean weighted kappa for interobserver agreement was 0.80 (range 0.77-0.84) for intensity and 0.21 (range 0.11-0.26) for extent. The subjective estimations of intensity correlated with results of image analysis (r = 0.61-0.66, p < 0.001), but the correlation between observers was stronger (r = 0.75-0.81) and correlated better with Gleason grade. Thus, subjective assessment of intensity can be done with a high level of reproducibility while estimation of staining extent is less reliable. Although educated pathologists were faster, the level of pathology training is not crucial for obtaining reproducible results in the analysis of TMA-based studies.

Tissue Microarray: A rapidly evolving diagnostic and research tool

Tissue microarray is a recent innovation in the field of pathology. A microarray contains many small representative tissue samples from hundreds of different cases assembled on a single histologic slide, and therefore allows high throughput analysis of multiple specimens at the same time. Tissue microarrays are paraffin blocks produced by extracting cylindrical tissue cores 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 arrayed into a single paraffin block. It can permit 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 use of limited and irreplaceable archival tissue samples. This versatile technique, in which data analysis is automated, facilitates retrospective and prospective human tissue studies. It is a practical and effective tool for high-throughput molecular analysis of tissues that is helping to identify new diagnostic and prognostic markers and targets in human cancers, and has a range of potential applications in basic research, prognostic oncology and drug discovery. This article summarizes the technical aspects of tissue microarray construction and sectioning, advantages, application, and limitations.

Identification of retinoic acid-regulated nuclear matrix-associated protein as a novel regulator of gastric cancer

BACKGROUND

Retinoic acid-regulated nuclear matrix-associated protein (RAMP) is a WD40 repeat-containing protein that is involved in various biological functions, but little is known about its role in human cancer. This study aims to delineate the oncogenic role of RAMP in gastric carcinogenesis.

METHODS

RAMP expression was examined by real-time quantitative RT-PCR, immunohistochemistry and western blotting. Inhibition of RAMP expression was performed by siRNA-mediated knockdown. The functional effects of RAMP on cell kinetics were measured by cell viability assay, colony formation assay and flow cytometry. Cell lines stably expressing RAMP were established to investigate the oncogenic effects of RAMP in vitro.

RESULTS

Ramp was readily expressed in all seven gastric cancer cell lines and was significantly increased in human gastric cancer tissues when compared with their adjacent non-cancerous tissues (P<0.001). In keeping with this, expression of RAMP protein was higher in gastric cancer tissues compared with their adjacent non-cancerous tissues, whereas moderate protein expression were noted in intestinal metaplasia. Knockdown of RAMP in gastric cancer cells significantly reduced cell proliferation (P<0.01) and soft agar colony formation (P<0.001), but induced apoptosis and G(2)/M arrest. In additional, knockdown RAMP induced cell apoptosis is dependent on functional accumulation of p53 and p21 and induction of cleaved caspases-9, caspases-3 and PARP. Strikingly, overexpression of RAMP promoted anchorage-independent cell growth in soft agar.

CONCLUSION

Our findings demonstrate that RAMP plays an oncogenic role in gastric carcinogenesis. Inhibition of RAMP may be a promising approach for gastric cancer therapy.

Validation of tissue microarray immunohistochemistry staining and interpretation in diffuse large B-cell lymphoma

Tissue microarrays (TMAs) show concordance with whole tissue sections in the immunohistochemical evaluation of tumor cells. However, potential inter-institutional variability among observers and immunohistochemical staining methods has not been fully addressed. We selected 21 cases of diffuse large B-cell lymphoma (DLBCL) to process for TMAs. Immunohistochemical stains were performed in 3 laboratories, and reviewed independently by 3 hematopathologists at the 3 institutions. Stains were scored on a 4-point scale. Statistical analyses of variation in the scoring among observers and among different institutions' stains were performed. Stains for CD3, CD10, CD20, BCL-2, BCL-6, MIB-1, and FOX-P1 revealed little variation among observers, with an average 51-82% complete agreement and 82-100% agreement +/- 1 numerical score. The rate of concordance when evaluating most stains performed in different laboratories was also relatively good, with an average of 55-72% complete agreement and 70-97% agreement +/- 1 score. However, scoring of MUM-1 and p53 stains showed wider variation, with an average of only 37 and 30% complete agreement among observers, and 11 and 45% agreement when stains from different institutions were examined. Further statistical analyses were performed to compare the observers' scoring of their own institution's stains (self-review) vs. observers' scoring of other institutions' stains (non-self). The agreement rate for the p53 stain was significantly higher when based on self-review (average 58% complete agreement) compared with an agreement rate of only 10.5% when based on a review of stains performed in another laboratory, non-self review, P < 0.01. This difference in the self- vs. non-self review was not seen when data for MUM-1 were analysed. In conclusion, most phenotypic markers used in the analysis of DLBCL can be evaluated in TMAs with adequate agreement among observers and laboratories. These include CD3, CD20, CD10, BCL-2, BCL-6, MIB-1, and FOX-P1. However, some markers, such as p53 and MUM-1, are more prone to inter-institutional variation. Variations in interpretation can be partially overcome by self-adjusted/adapt tendency, as seen with p53. Especially with newly developed markers, such as MUM-1, the development of standardized techniques for staining and interpretation is critical to reduce inter-observer variability.

Tissue Microarray: A rapidly evolving diagnostic and research tool

Tissue microarray is a recent innovation in the field of pathology. A microarray contains many small representative tissue samples from hundreds of different cases assembled on a single histologic slide, and therefore allows high throughput analysis of multiple specimens at the same time. Tissue microarrays are paraffin blocks produced by extracting cylindrical tissue cores 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 arrayed into a single paraffin block. It can permit 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 use of limited and irreplaceable archival tissue samples. This versatile technique, in which data analysis is automated, facilitates retrospective and prospective human tissue studies. It is a practical and effective tool for high-throughput molecular analysis of tissues that is helping to identify new diagnostic and prognostic markers and targets in human cancers, and has a range of potential applications in basic research, prognostic oncology and drug discovery. This article summarizes the technical aspects of tissue microarray construction and sectioning, advantages, application, and limitations.

Validation of tissue microarray technology in ovarian cancer: results from the Nurses' Health Study

BACKGROUND

Tissue microarrays (TMAs) allow high-throughput evaluation of protein expression from archived tissue samples. We identified characteristics specific to ovarian cancer that may influence TMA interpretation.

METHODS

TMAs were constructed using triplicate core samples from 174 epithelial ovarian cancers. Stains for p53, Ki-67, estrogen receptor-alpha, progesterone receptor, Her-2, WT-1, cytokeratin 7, and cytokeratin 20 were evaluated by intraclass correlation coefficients, Spearman correlation coefficients, the effect of sample age, and tumor histology on the ability to score the cores, and inter-rater reliability.

RESULTS

The interclass correlation coefficient and the mean Spearman correlation coefficients among 3 cores were > or = 0.91 and 0.87, respectively. Tissue age and tumor histology were not predictive of an inability to evaluate stains, but borderline tumors had a 2 to 4-fold increase in the risk of having uninterpretable cores over invasive tumors. There was moderate to substantial concordance between the two pathologists for estrogen receptor-alpha [Cohen's Kappa (kappa), 0.79] and Ki-67 (kappa, 0.52). The prevalence of positive staining cells by histologic type was comparable with previous studies.

CONCLUSION

TMA is a valid method for evaluating antigen expression in invasive ovarian cancer but should be used with caution for borderline tumors. We suggest several methods of quality control based on intercore comparisons and show that some antigens may be affected by age of the samples.

BCCIP as a prognostic marker for radiotherapy of laryngeal cancer

BACKGROUND

Recent studies have shown that BCCIP (BRCA2 and CDKN1A interacting protein) is essential for maintaining the transactivation activity of wild type p53. We analyzed the expression of BCCIP and p53 in a cohort of laryngeal cancer treated with radiotherapy and assessed whether BCCIP and p53, alone or in combination, would correlate with local control and overall survival.

METHODS

One hundred twenty-three patients treated between 1975 and 2000 for early stage (stages I and II) squamous cell carcinoma of the larynx were included in the study. Treatment consisted of radiation therapy (RT) with standard fields and fractionation to a median dose of 66Gy. Tissue was collected from pre-RT biopsies and constructed in a tissue microarray, and BCCIP expression and p53 expression were determined using immunohistochemistry.

RESULTS

Loss of expression of BCCIP in combination with normal p53 (negative p53 staining) was associated with local recurrence (RR 2.04; 95% CI 0.99-4.56, p=0.05) and poor overall survival (RR 2.09; 95% CI 1.21-4.00, p=0.008) compared to patients who did express BCCIP. Expression of BCCIP or p53 alone was not found to be independently associated with benefits in local control or overall survival.

CONCLUSIONS

This study provides clinical evidence that BCCIP contributes to outcomes in patients with laryngeal cancer treated with RT. This benefit may be a result of increased radiosensitivity in patients who have functional BCCIP and p53. These data may be used to identify sub-groups of laryngeal cancer patients who are more likely to be cured with radiotherapy.

Cold-inducible RNA-binding protein bypasses replicative senescence in primary cells through extracellular signal-regulated kinase 1 and 2 activation

Embryonic stem cells are immortalized cells whose proliferation rate is comparable to that of carcinogenic cells. To study the expression of embryonic stem cell genes in primary cells, genetic screening was performed by infecting mouse embryonic fibroblasts (MEFs) with a cDNA library from embryonic stem cells. Cold-inducible RNA-binding protein (CIRP) was identified due to its ability to bypass replicative senescence in primary cells. CIRP enhanced extracellular signal-regulated kinase 1 and 2 (ERK1/2) phosphorylation, and treatment with an MEK inhibitor decreased the proliferation caused by CIRP. In contrast to CIRP upregulation, CIRP downregulation decreased cell proliferation and resulted in inhibition of phosphorylated ERK1/2 inhibition. This is the first evidence that ERK1/2 activation, through the same mechanism as that described for a Val12 mutant K-ras to induce premature senescence, is able to bypass senescence in the absence of p16(INK4a), p21(WAF1), and p19(ARF) upregulation. Moreover, these results show that CIRP functions by stimulating general protein synthesis with the involvement of the S6 and 4E-BP1 proteins. The overall effect is an increase in kinase activity of the cyclin D1-CDK4 complex, which is in accordance with the proliferative capacity of CIRP MEFs. Interestingly, CIRP mRNA and protein were upregulated in a subgroup of cancer patients, a finding that may be of relevance for cancer research.

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.

AQUA analysis of thymidylate synthase reveals localization to be a key prognostic biomarker in 2 large cohorts of colorectal carcinoma

CONTEXT

Increased thymidylate synthase expression is a marker for decreased survival in colorectal cancer.

OBJECTIVE

Thymidylate synthase localizes to both the nucleus and cytoplasm, but how the relationship of these expression levels affects colon cancer outcome has yet to be determined.

DESIGN

Using AQUA, we assessed prognosis of thymidylate synthase expression as a function of subcellular localization in 2 retrospective cohorts of colorectal carcinoma. We used the first cohort (n = 599) as a training set, subsequently validating optimal expression cut points in the second cohort (n = 447).

RESULTS

A significant association between decreased 5-year disease-specific survival and increased nuclear expression (16% decreased survival [72% to 56%] for the top 60% of nuclear-expressing tumors [P < .001]) and cytoplasmic expression (12% decreased survival [70% to 58%] for the top 54% of cytoplasmic-expressing tumors [P = .02]) was observed for the training set. A higher nuclear to cytoplasmic ratio also correlated significantly with decreased survival (15% decreased survival [66% to 51%] for the top 25% of tumors [P < .001]). Applying these findings to the validation set, as a function of time to recurrence, only the ratio (P = .03 [expression ratio]; P = .18 [nuclear]; P = .71 [cytoplasmic]) showed a significant association with decreased time to recurrence. Additionally, the expression ratio significantly added to the prognostic value given by the primary tumor pathologic classification and nodal status.

CONCLUSIONS

These data suggest the relationship of nuclear to cytoplasmic thymidylate synthase expression, given as a ratio of continuous AQUA scores, to be a strong predictor of colon cancer survival.