Tissue microarrays for rapid linking of molecular changes to clinical endpoints

A practical guide to constructing and using tissue microarrays

Tissue microarray (TMA) technology is a robust "high throughput" method of tissue analysis, whereby a large number of patient samples can be examined in a short time using a minimum number of slides. In a TMA, cylinders of tissue are cored out of formalin-fixed, paraffin-embedded tissue blocks and slotted in a regular grid pattern into a blank recipient paraffin wax block. The TMA block is then cut using a standard laboratory microtome. Sections generated are suitable for all in situ techniques, such as immunohistochemistry (IHC) and in situ hybridisation, using essentially the same protocols as are used in conventional sections. The principle advantages of TMAs are that they save valuable biological material and ensure more reproducible reaction conditions while at the same time reducing re-agent costs and laboratory processing. Immunohistochemical studies designed to examine the prognostic utility of TMAs compared with large sections have generally found that they are comparable.

From gene to clinic: TMA-based clinical validation of molecular markers in prostate cancer

Current high-throughput screening techniques using DNA arrays have identified hundreds of new candidate biomarkers for diagnosis and risk prediction of prostate cancer. Large-scale analysis of clinical prostate cancer specimens is a key prerequisite for the validation of these genes. We have constructed a tissue microarray from more than 2,500 prostate cancers with full histo-pathological and clinical long-term follow-up data and analyzed expression and gene copy number patterns of 16 different candidate markers for their ability to predict prostate cancer progression and patient prognosis. The best candidates were used to extend established clinical prediction tools (nomograms) that were based on nonmolecular data only, such as prostate-specific antigene (PSA), clinical stage, and histological grading (Gleason grade). Using this approach, we could identify ANXA3 as an independent marker, which was capable of increasing the accuracy of the clinical nomogram, thereby fulfilling the criteria of a novel prognostic prostate cancer marker. This approach of integrating large-scale clinical and molecular variables may provide a new paradigm for the use of molecular profiling to predict the clinical outcome in prostate cancer.

Quality aspects of TMA analysis

The quality of a TMA experiment can only be as good as the worst step in the entire process. Making and analyzing of tissue microarrays (TMAs) is a complex process involving tissue sample acquisition and preparation, expert histological diagnosis, long-term collection of clinical data, development of suitable laboratory protocols, the microscopic analysis, and the statistical analysis of the experiment. The quality of all these factors equally influences the outcome of TMA studies.

Systematic assessment of protein phenotypes characterizing high-grade tumour budding in mismatch repair-proficient colorectal cancer

AIMS

A tumour bud is defined as a single tumour cell or tumour cell cluster of up to five cells at the invasive tumour front. Significant differences in survival have been detected in colorectal cancer patients with low- compared to high-grade budding. The aim of this study was to identify potential multi-marker phenotypes characterizing low- and high-grade budding in mismatch repair (MMR)-proficient colorectal cancer.

METHODS AND RESULTS

Established and promising prognostic proteins such as epidermal growth factor receptor (EGFR), pERK, RHAMM, RKIP, beta-catenin, E-cadherin, pAKT, p16, p21, Ki67, Bcl-2, vascular endothelial growth factor (VEGF), apoptotic protease activating factor-1 (APAF-1), MUC1, EphB2, matrix metalloproteinase 7, pSMAD2, CDX2, laminin5gamma2 and MST1 were analysed on 208 MMR-proficient colorectal cancers with complete clinicopathological data. The most accurate markers for predicting high-grade budding (more than six tumour buds) were EphB2 (P < 0.001), Bcl-2 (P < 0.001), RKIP (P < 0.001), E-cadherin (P = 0.004), laminin5gamma2 (P = 0.004) and APAF-1 (P = 0.005). On multivariable analysis, only loss of Bcl-2 (P < 0.001) and EphB2 (P < 0.001) were independent predictors of high-grade budding. Bcl-2-/EphB2- tumours were more frequently poorly differentiated (P < 0.001), of advanced pT stage (P = 0.002), lymph node positive (P = 0.023), presented vascular (P = 0.053) and lymphatic invasion (P = 0.005) and had a negative impact on patient survival (P = 0.012).

CONCLUSIONS

The multi-marker phenotype EphB2-/Bcl-2- is an independent predictor of high-grade budding and implies increased aggressive behaviour in MMR-proficient colorectal cancer.

Cystatin M loss is associated with the losses of estrogen receptor, progesterone receptor, and HER4 in invasive breast cancer

Introduction

This study was aimed at understanding the clinicopathological significance of cystatin M loss, and investigating possible factors responsible for cystatin M loss in breast cancer.

Methods

The expression of estrogen receptor (ER), progesterone receptor (PR), HER2, HER4, and cystatin M was retrospectively analyzed using immunohistochemistry in 117 patients with ductal carcinoma in situ (DCIS) and in 175 patients with invasive breast cancer (IBC). The methylation status of CST6 gene encoding cystatin M was evaluated using methylation-specific polymerase chain reaction (PCR) in formalin-fixed paraffin-embedded tissues from 292 participants and using pyrosequencing in fresh-frozen tumor and matched normal tissues from 51 IBC patients.

Results

Cystatin M loss was found in 9 (8%) of 117 patients with DCIS and in 99 (57%) of 175 with invasive breast cancer (IBC) (P < 0.0001). Cystatin M loss was found in 58 (57%) of 101 HER2-negative IBCs and in 41 (55%) of 74 HER2-positive IBCs, and this difference was not statistically significant (P = 0.97). However, cystatin M loss was significantly associated with the loss of ER (P = 0.01), PR (P = 0.002), and HER4 (P = 0.003) in IBCs. Cystatin M loss occurred in 34 (76%) of the 45 HER4-negative IBCs and in 65 (50%) of the 130 HER4-positive IBCs. Multivariate analysis showed that cystatin M loss occurred at a 3.57 times (95% CI = 1.28 to 9.98; P = 0.01) higher prevalence in the triple-negative IBCs of ER, PR, and HER4 than in other subtypes, after adjusting for age. The quantity of CST6 methylation was associated with ER loss (P = 0.0002) in IBCs but not with the loss of PR (P = 0.64) or HER4 (P = 0.87).

Conclusions

The present study suggests that cystatin M loss may be associated with the losses of ER, PR, and HER4 in IBC.

Limitations of tissue microarrays compared with whole tissue sections in survival analysis

Tissue microarray (TMA) is a promising technique in the evaluation of immunohistochemical markers in tumors and may be used as an alternative for whole sections. However, only a few studies have correlated a clinical outcome with both TMA and results obtained from whole sections. This study compared immunostaining for Ki-67 and p16 in TMA (3 cores from each specimen) and whole sections of 171 cases of stage III epithelial ovarian cancer with clinical data. A high expression of Ki-67 was identified in 85.0, 85.5, 85.8, 90.5 and 84% of cores 1, 2 and 3, TMAs and whole tissue sections, respectively. A high p16 expression was found in 36.5, 31.4, 30.3, 46.3 and 31.0% of cores 1, 2 and 3, TMAs and whole tissue sections, respectively. The high expression of Ki-67 and p16 in whole tissue sections significantly correlated with that of Ki-67 and p16 in core 1 (P<0.0001 and P<0.0001, respectively), core 2 (P<0.0001 and P<0.0001, respectively), core 3 (P<0.0001 and P<0.0001, respectively), and TMAs (P<0.0001 and P<0.0001, respectively). In univariate analysis, a high expression of Ki-67 and p16 in two of the cores; TMA and the whole tissue sections were significantly correlated to disease-related survival (Ki-67: P=0.008, 0.012, 0.012 and 0.0001, respectively, and p16: P=0.0007, 0.0005, 0.0008 and 0.005, respectively). However, in the multivariate analysis only Ki-67 on whole tissue sections retained an independent prognostic significance (P=0.025). We concluded that more studies, with a higher number of cores, are necessary to determine the efficacy of TMA in reflecting the prognostic value of different antibodies. Morever, evaluation of this method is crucial for each type of tumor and each separate antigen. It is also essential to confirm the clinical correlations on the whole sections before investigating the same parameters on TMA.

The stem cell gene "inhibitor of differentiation 1" (ID1) is frequently expressed in non-small cell lung cancer

AIMS

Inhibitor of differentiation 1 (ID1) plays a role in cellular differentiation, proliferation, angiogenesis and tumor invasion. As shown recently, ID1 is positively regulated by the tyrosine kinase SRC in lung carcinoma cell lines and with that appears as a potential new therapeutic target in non-small cell carcinoma (NSCLC). To substantiate this hypothesis we examined ID1, SRC and matrix metalloproteinase-9 (MMP-9) immunohistochemically in human NSCLC specimens.

METHODS

From 61 consecutive patient tissue samples of a tumor tissue bank a one core tissue microarray (TMA) was produced and whole slide tissue samples of preinvasive lesions used. The staining of commercial antibodies was assessed by the H-score. Statistical analyses based on Spearman's rank correlation coefficient.

RESULTS

ID1 was expressed in the nucleus in 70% of squamous cell carcinomas and 50% of non-squamous cell carcinomas and in vascular endothelium of non-tumor tissue. Cytoplasmic staining was found in all samples for SRC and in 93% for MMP-9. ID1-positive tissue samples co-expressed SRC and MMP-9 in 94%. In non-squamous cell carcinomas, H-scores of ID1 and SRC correlated with each other (p=0.04). H-score of MMP-9 correlated with tumor grade (p=0.04). The carcinoma findings were reflected in preinvasive lesions.

CONCLUSIONS

We describe for the first time the immunohistochemical expression of ID1 in the majority of NSCLC samples. The almost general co-expression of ID1, SRC and MMP-9 supports their cooperation in vivo and warrants further investigation of ID1 as a therapeutic target.

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.

Overexpression of carbonic anhydrase IX (CAIX) in vulvar cancer is associated with tumor progression and development of locoregional lymph node metastases

Carbonic anhydrase IX (CAIX) is a strictly membranous expressed metalloenzyme involved in cell adhesion, pH homeostasis, and cancer progression. The protein is specifically overexpressed in a wide variety of malignant tumors. This study was designed to assess the role of CAIX in primary vulvar cancer. One hundred forty-two well-characterized primary vulvar carcinomas were analyzed on a tissue microarray (TMA). Three tissue cores were sampled from each tumor. CAIX expression was determined by immunohistochemistry, using a four-step scoring system. To determine CAIX expression in benign vulvar tissue, we constructed a TMA with 120 samples of normal mucosa and non-neoplastic diseases. CAIX expression was found in 77/135 (57%) of all assessable vulvar cancer specimens and 48 (35.5%) exhibited a moderate or strong expression. CAIX expression in vulvar carcinomas was significantly stronger compared to non-neoplastic vulvar tissue (p < 0.001). High levels of CAIX expression were related to pT stage (p < 0.01), tumor size (p < 0.01), depth of invasion (p < 0.05), as well as inguinal lymph node metastases (p < 0.05). There was also a trend towards shorter recurrence-free patient survival in CAIX-positive compared to CAIX-negative vulvar cancers. CAIX staining results in different tissue cores from the same tumor were homogeneous, raising the possibility of a hypoxia-independent expression. In conclusion, CAIX is overexpressed in the majority of vulvar carcinomas with relationships to advanced tumor stages and development of lymph node metastases. Our data support the potential therapeutic benefit of newly developed targeting antibodies in advanced vulvar cancer.

Evidence for distinct alterations in the FGF axis in prostate cancer progression to an aggressive clinical phenotype

Multiple fibroblast growth factor (FGF) axis alterations are known to occur in prostate cancer. Here we simultaneously profiled key components of this axis to determine their relevance in disease progression. An optimized immunohistochemistry protocol was used in expression analysis of FGF2, FGF8, FGFR1, FGFR4, and Sef (similar expression to FGF) in a single TMA of prostate cancer. FGF ligands and receptors were overexpressed in cancers compared to benign samples (p < 0.0001), while Sef expression was reduced (p < 0.0001). There was a positive association between higher grades and increased FGFR4 (p = 0.02), FGF2, and FGF8 (p = 0.002 and p < 0.0001). Sef expression was progressively lower with increasing grade (p = 0.005). Clinical stage was positively associated with FGF2, FGF8, and FGFR4 expression (p = 0.005, 0.03, and 0.012) but not with FGFR1 or Sef expression. Only reduced Sef was associated with bone metastasis (p = 0.02) and was also predictive of subsequent metastasis in initially localized tumours (p = 0.004). Down-regulation of Sef and increased FGFR4 were also the only independent variables associated with disease-specific survival (HR 1.73, p = 0.04 and HR 0.56, p = 0.01). In in vitro studies, silencing Sef enhanced the cell response to FGFs (p < 0.001) and substantially mitigated the effectiveness of an FGFR1 inhibitor. Conversely, increased Sef blocked the response to FGFs and had a comparable suppressive effect to the inhibitor. This study demonstrates that increased FGFR4 and reduced Sef may be critical FGF alterations associated with prostate cancer progression. Sef may also have a role in the tumour response to FGFR inhibition and warrants further investigation in this context.

Use and validation of epithelial recognition and fields of view algorithms on virtual slides to guide TMA construction

While tissue microarrays (TMAs) are a form of high-throughput screening, they presently still require manual construction and interpretation. Because of predicted increasing demand for TMAs, we investigated whether their construction could be automated. We created both epithelial recognition algorithms (ERAs) and field of view (FOV) algorithms that could analyze virtual slides and select the areas of highest cancer cell density in the tissue block for coring (algorithmic TMA) and compared these to the cores manually selected (manual TMA) from the same tissue blocks. We also constructed TMAs with TMAker, a robot guided by these algorithms (robotic TMA). We compared each of these TMAs to each other. Our imaging algorithms produced a grid of hundreds of FOVs, identified cancer cells in a stroma background and calculated the epithelial percentage (cancer cell density) in each FOV. Those with the highest percentages guided core selection and TMA construction. Algorithmic TMA and robotic TMA were overall approximately 50% greater in cancer cell density compared with Manual TMA. These observations held for breast, colon, and lung cancer TMAs. Our digital image algorithms were effective in automating TMA construction.

Low level HER2 overexpression is associated with rapid tumor cell proliferation and poor prognosis in prostate cancer

PURPOSE

The HER2 oncogene is involved in the biology of many different tumor types and serves as a prognostic marker and a therapeutic target in breast cancer. In contrast to breast cancer, studies on Her2 overexpression and gene amplification in prostate cancer have yielded different results. The purpose of this study was to learn more on the prevalence and clinical significance of HER2 amplification and overexpression in prostate cancer.

EXPERIMENTAL DESIGN

A tissue microarray containing >2,000 prostate cancers with follow-up data was used. Tissue microarray sections were analyzed on protein and DNA level using two different antibodies (HercepTest, DAKO; Novocastra NCL-CB11) and fluorescence in situ hybridization.

RESULTS

Immunohistochemical analyses showed highly similar results for both antibodies. Detectable Her2 immunostaining was observed in 17.2% for the HercepTest and in 22.5% for the Novocastra antibody with the vast majority of cases showing 1+ or 2+ staining. For both antibodies (HercepTest/Novocastra), significant associations were found between positive staining and high Gleason grade (P < 0.0001, both), advanced pT stage (P < 0.0001/P = 0.0015), rapid tumor cell proliferation (P = 0.0004/P = 0.0071), and tumor recurrence (P < 0.0001, both). HER2 amplification was only found in 1 of 2,525 analyzable cases (0.04%).

CONCLUSIONS

Low-level Her2 overexpression occurs at relevant frequency in prostate cancer and in the absence of gene amplification. Increased Her2 expression may potentially lead to an aggressive behavior of tumor cells through the stimulation of tumor cell proliferation because Her2 staining was shown to be significantly associated with Ki67 labeling index. These data argue for reconsidering anti-Her2 therapy, possibly with modified approaches.

Loss of the CBX7 protein expression correlates with a more aggressive phenotype in pancreatic cancer

Polycomb group (PcG) proteins function as multiprotein complexes and are part of a gene regulatory mechanism that determines cell fate during normal and pathogenic development. Several studies have implicated the deregulation of different PcG proteins in neoplastic progression. Pancreatic ductal adenocarcinoma is an aggressive neoplasm that follows a multistep model of progression through precursor lesions called pancreatic intraepithelial neoplasia (PanIN). Aim of this study was to investigate the role of PcG protein CBX7 in pancreatic carcinogenesis and to evaluate its possible diagnostic and prognostic significance. We analysed by immunohistochemistry the expression of CBX7 in 210 ductal pancreatic adenocarcinomas from resection specimens, combined on a tissue microarray (TMA) including additional 40 PanIN cases and 40 normal controls. The results were evaluated by using receiver operating characteristic (ROC) curve analysis for the selection of cut-off scores and correlated to the clinicopathological parameters of the tumours and the outcome of the patients. Expression of E-cadherin, a protein positively regulated by CBX7, was also assessed. A significantly differential, and progressively decreasing CBX7 protein expression was found between normal pancreatic tissue, PanINs and invasive ductal adenocarcinoma. Loss of CBX7 expression was associated with increasing malignancy grade in pancreatic adenocarcinoma, whereas the maintenance of CBX7 expression showed a trend toward a longer survival. Moreover, loss of E-cadherin expression was associated with loss of CBX7 and with a trend towards worse patient survival. These results suggest that CBX7 plays a role in pancreatic carcinogenesis and that its loss of expression correlates to a more aggressive phenotype.

Predictive significance of bone sialoprotein and osteopontin for bone metastases in resected Chinese non-small-cell lung cancer patients: a large cohort retrospective study

BACKGROUND

Bone is one of the most common sites of metastasis in patients with non-small-cell lung cancer (NSCLC). Over-expression of bone sialoprotein (BSP) and osteopontin (OPN) in tumour samples has shown prognostic significance in bone metastasis (BM) of breast and prostate cancer, respectively. However, their importance in BM of NSCLC has not been verified. Therefore, we planned a large cohort retrospective study to investigate the relationship between the expression of these two biomarkers (BSP and OPN) and BM in surgically resected NSCLC patients.

METHODS

180 completely resected NSCLC patients were included in this study. 40 patients subsequently developed BM. Paraffin-embedded primary tumour tissues of patients were supplied to produce a tissue microarray, and immunohistochemistry method was used for evaluation of the expression of BSP and OPN. Different expressions of these two biomarkers among BM group and non-BM group were estimated by chi(2) test. BM-free survival was analyzed by Kaplan-Meier method. The prognostic impact of clinicopathologic variables and biomarker expression was evaluated by Cox proportional hazards model.

RESULTS

BSP expression was associated with BM (p=0.007), whereas OPN expression did not reach statistical significance (p=0.245). Univariate analysis showed that expression of BSP (p=0.010) and N staging (p<0.005) was associated with BM-free survival. Multivariate analyses showed BSP expression (HR=3.322, p=0.003), N staging (HR=1.879, p=0.001), and T staging (HR=1.618, p=0.024) were independent prognostic factors for BM.

CONCLUSIONS

BSP protein expression in the primary resected NSCLC is strongly associated with BM and could be used to identify high-risk patients. Correlation of OPN protein expression and BM needs further investigation.

IGFBP2 and IGFBP3 protein expressions in human breast cancer: association with hormonal factors and obesity

PURPOSE

The insulin-like growth factor (IGF) signaling system is involved in breast cancer initiation and progression. The prognostic relevance of tumor expression patterns of IGFI-related proteins remains poorly understood. This study associates the expression of selected IGF proteins with breast tumor and patient characteristics.

EXPERIMENTAL DESIGN

IGFI, IGFI receptor, IGF-binding protein (IGFBP)2, and IGFBP3 expression was measured in 855 primary breast carcinomas by immunohistochemistry using tissue microarrays. We investigated the association of tumor and nodal stage, grade, hormone receptor status, HER2 gene amplification, menopausal status, body mass index, and survival with IGF protein expression.

RESULTS

In contrast to IGFI, the expression of IGFI receptor, IGFBP2, and IGFBP3 was associated with estrogen receptor status. In addition, IGFBP3 was positively correlated with body mass index and premenopausal status. Importantly, IGFBP2 was an independent and positive predictor of overall survival (hazard ratio, 0.48; 95% confidence interval, 0.24-0.95; P = 0.04). There was a weak suggestion for IGFBP2 and overweight to modify each other's effect on survival.

CONCLUSIONS

According to these results, which need confirmation in larger patient series, the prognostic relevance of IGFBP2 and IGFBP3 protein expressions in breast cancer may depend on the hormonal context and body weight.

The role of vascular CXCR4 expression in colorectal carcinoma

AIMS

The chemokine receptor CXCR4 plays a prominent role in the biology of many different tumours, promoting angiogenesis and metastasis. The impact of CXCR4 expression on tumour biology has been described in various gastrointestinal malignancies, but data on its in situ expression and clinicopathological correlations are sparse. Using a novel specific rabbit anti-CXCR4 antibody, the aim was to assess CXCR4 expression immunohistochemically on tissue microarrays generated from 402 colorectal cancers (CRCs) and compare it with CXCL12 expression and various clinicopathological parameters.

METHODS AND RESULTS

CXCR4-expressing tumour cells were observed in 31% of the cases, and expression correlated only with blood vessel invasion (P = 0.049). Furthermore, CXCR4 was found in tumour microvessels in 25% of CRCs. This pattern of CXCR4 expression correlated significantly with T- (P = 0.008), N- (P = 0.009), M- (P = 0.043), L- (P = 0.014) and V-category (P = 0.043) as well as with International Union Against Cancer (UICC) stage (P = 0.001). Furthermore, in node negative CRCs, vascular CXCR4 expression was an independent adverse prognostic factor [hazard ratio 2.87 (1.31-6.29), P = 0.009]. No correlation with CXCL12 expression was found.

CONCLUSIONS

Our data provide evidence that CXCR4 plays an important role in tumour angiogenesis of CRC. Therefore, the CXCR4 pathway is a promising therapeutic target for anti-angiogenic therapies in CRC.

Assessing the application of tissue microarray technology to kidney research

Tissue microarray (TMA) is a new high-throughput method that enables simultaneous analysis of the profiles of protein expression in multiple tissue samples. TMA technology has not previously been adapted for physiological and pathophysiological studies of rodent kidneys. We have evaluated the validity and reliability of using TMA to assess protein expression in mouse and rat kidneys. A representative TMA block that we have produced included: (1) mouse and rat kidney cortex, outer medulla, and inner medulla fixed with different fixatives; (2) rat kidneys at different stages of development fixed with different fixatives; (3) mouse and rat kidneys with different physiological or pathophysiological treatments; and (4) built-in controls. As examples of the utility, immunostaining for cyclooxygenase-2, renin, Tamm Horsfall protein, aquaporin-2, connective tissue growth factor, and synaptopodin was carried out with kidney TMA slides. Quantitative analysis of cyclooxygense-2 expression in kidneys confirms that individual cores provide meaningful representations comparable to whole-kidney sections. These studies show that kidney TMA technique is a promising and useful tool for investigating the expression profiles of proteins of interest in rodent kidneys under different physiological and pathophysiological conditions.

Recipient block TMA technique

New high-throughput screening technologies have led to the identification of hundreds of genes with a potential role in cancer or other diseases. One way to prioritize the leads obtained in such studies is to analyze a large number of tissues for candidate gene expression. The TMA methodology is now an established and frequently used tool for high-throughput tissue analysis. The recipient block technology is the "classical" method of TMA making. In this method, minute cylindrical tissue punches typically measuring 0.6 mm in diameter are removed from donor tissue blocks and are transferred into empty "recipient" paraffin blocks. Up to 1,000 different tissues can be analyzed in one TMA block. The equipment is affordable and easy to use in places where basic skills in histology are available.

Applications of tissue microarray technology

Tissue microarrays (TMAs) have become a standard tool for tissue-based research during the last decade. In cancer research, depending on the available data attached to the arrayed tissue, three main types of arrays are commonly manufactured. Prevalence TMAs have no further data available and are suited to estimate the frequency of the occurrence of a particular alteration. Progression arrays include tissues of different stages of disease, and are instrumental to study the role of a marker protein for tumor initiation, progression, or metastatic growth. Prognosis TMAs contain tissues with patient follow-up data. These TMAs are the key to uncover the clinical impact of molecular markers. In combination with normal tissue arrays representing healthy tissues, prevalence, progression, and prognosis TMAs allow for a rapid and comprehensive analysis of molecular markers in human cancers. TMAs are also successfully used for many noncancer applications, such as Alzheimer's or inflammatory disease research.

Representativity of TMA studies

The smaller the portion of a tumor sample that is analyzed becomes, the higher is the risk of missing important histological or molecular features that might be present only in a subset of tumor cells. Many researchers have, therefore, suggested using larger tissue cores or multiple cores from the same donor tissue to enhance the representativity of TMA studies. However, numerous studies comparing the results of TMA studies with the findings from conventional large sections have shown that all well-established associations between molecular markers and tumor phenotype or patient prognosis can be reproduced with TMAs even if only one single 0.6 mm tissue spot is analyzed. Moreover, the TMA technology has proven to be superior to large section analysis in finding new clinically relevant associations. The high number of samples that are typically included in TMA studies, and the unprecedented degree of standardization during TMA experiments and analysis often give TMA studies an edge over traditional large-section studies.

Chromosome 8p deletions and 8q gains are associated with tumor progression and poor prognosis in prostate cancer

PURPOSE

Deletions of 8p and gains of 8q belong to the most frequent cytogenetic alterations in prostate cancer. The target genes of these alterations and their biological significance are unknown.

EXPERIMENTAL DESIGN

To determine the relationship between chromosome 8 changes, and prostate cancer phenotype and prognosis, a set of 1.954 fully annotated prostate cancers were analyzed in a tissue microarray format by fluorescence in situ hybridization.

RESULTS

Both 8p deletions and 8q gains increased in number during different stages of prostate cancer progression. 8p deletions/8q gains were found in 26.1%/4.8% of 1,239 pT(2) cancers, 38.5%/9.8% of 379 pT(3a) cancers, 43.5%/8.9% of 237 pT(3b) cancers, 40.7%/14.8% of 27 pT(4) cancers, 39.1%/34.8% of 23 nodal metastases, 51.9%/33.3% of 27 bone metastases, and 45.5%/59.9% of 22 hormone refractory cancers (P < 0.0001 each). Both 8p deletions and 8q gains were also significantly associated with high Gleason grade and with each other (P < 0.0001 each). In primary tumors, 8p deletions were seen in only 27.3% of 1,882 cancers without 8q gain but in 57.4% of 122 tumors with 8q gain (P < 0.0001). Among cancers treated with radical prostatectomy, 8p deletions (P = 0.003) and 8q gains (P = 0.02) were associated with biochemical tumor recurrence. However, multivariate analysis (including prostate-specific antigen, pT/pN stage, Gleason score, and surgical margin status) did not reveal any statistically independent effect of 8p or 8q alterations on biochemical tumor recurrence.

CONCLUSIONS

8p deletions and 8q gains are relatively rare in early stage prostate cancer but often develop during tumor progression. The prognostic effect does not seem to be strong enough to warrant clinical application.

ErbB family immunohistochemical expression in colorectal cancer patients with higher risk of recurrence after radical surgery

PURPOSE

Investigate ErbB family expression in colorectal cancer patients with higher risk of recurrence after surgical treatment.

METHODS

We studied 109 individuals with high risk stage II and stage III patients submitted to radical surgery. ErbB expression was assessed by tissue microarray technique.

RESULTS

The immunohistochemical expression was considered positive for EGFR, ErbB2, ErbB3, ErbB4 membrane, and ErbB4 cytoplasmic in respectively 57.8%, 8.3%, 69.7%, 11%, and 19.3% of patients. ErbB3 negative expression was associated with lymphovascular invasion. EGFR, ErbB2, and cytoplasmic ErbB4 expression was not associated with prognosis. Membranous positive ErbB4 expression was an independent prognostic factor for recurrence. ErbB3 negative expression was an independent prognostic factor for recurrence and survival in the multivariate analysis.

CONCLUSIONS

The immunohistochemical expression of ErbB3 and ErbB4 may identify a subgroup with stage II and III colorectal cancer at higher risk of recurrence.

Impact of BCL2 and p53 on postmastectomy radiotherapy response in high-risk breast cancer. A subgroup analysis of DBCG82 b&c

PURPOSE

To examine p53 and BCL2 expression in high-risk breast cancer patients randomized to postmastectomy radiotherapy (PMRT).

PATIENTS AND METHODS

The present analysis included 1 000 of 3 083 high-risk breast cancer patients randomly assigned to PMRT in the DBCG82 b&c studies. Tissue microarray sections were stained with immunohistochemistry for p53 and BCL2. Median potential follow-up was 17 years. Clinical endpoints were locoregional recurrence (LRR), distant metastases (DM), overall mortality, and overall survival (OS). Statistical analyses included Kappa statistics, chi(2) or exact tests, Kaplan-Meier probability plots, Log-rank test, and Cox univariate and multivariate regression analyses.

RESULTS

p53 accumulation was not significantly associated with increased overall mortality, DM or LRR probability in univariate or multivariate Cox regression analyses. Kaplan-Meier probability plots showed reduced OS and improved DM and LRR probabilities after PMRT within subgroups of both p53 negative and p53 positive patients. Negative BCL2 expression was significantly associated with increased overall mortality, DM and LRR probability in multivariate Cox regression analyses. Kaplan-Meier probability plots showed a significantly improved overall survival after PMRT for the BCL2 positive subgroup, whereas practically no survival improvement was seen after PMRT for the BCL2 negative subgroup. In multivariate analysis of OS, however, no significant interaction was found between BCL2 and randomization status. Significant reductions in LRR probability after PMRT were recorded within both the BCL2 positive and BCL2 negative subgroups.

CONCLUSION

p53 was not associated with survival after radiotherapy in high-risk breast cancer, but BCL2 might be.

Tissue microarrays compared with whole sections and biochemical analyses. A subgroup analysis of DBCG 82 b&c

INTRODUCTION

The tissue microarray (TMA) technique comprises the potential of significantly reducing time and tissue spent on slicing and performing immunohistochemical (IHC) stainings of paraffin-embedded tumor tissue. Tissue heterogeneity is an argument against using TMAs, which has been dealt with by increasing the size and number of cores punched from each tumor. No consensus exists on the most optimal size, number, and position of TMA cores in the donor paraffin block and no information exist regarding agreement between TMA cores from two different paraffin blocks from the same tumor or between TMA cores and biochemical analyses.

PATIENTS AND METHODS

A central and a peripheral 1mm core and a whole section from each of 54 paraffin blocks from 27 breast cancers included in a one-institution cohort, and a single 1mm central TMA core, from each breast tumor from 1000 patients included in the DBCG82 b&c trials, were IHC stained for ER, PgR and HER2. In addition, ER and PgR were measured in the DBCG82 b&c trials by a biochemical analysis. Statistical analyses included Kappa statistics, Kaplan-Meier survival curves, Log-rank tests, and Cox regression hazards analyses.

RESULTS AND CONCLUSION

IHC stainings for ER, PgR, and HER2 showed a substantial agreement between a single 1mm TMA core and the corresponding whole section, between central and peripheral cores, and between cores from two different paraffin blocks from the same tumor. In addition, a fine agreement was found for ER and PgR between IHC stainings of TMA cores and biochemical analyses. Divergence between IHC and biochemical analyses was predominantly due to the chosen thresholds. IHC staining of one 1mm core from each tumor revealed a significant independent prognostic value of PgR and HER2 on overall survival. In conclusion, IHC stainings for ER, PgR, and HER2 of just a single 1mm TMA core seems to be sufficient, as no significant heterogeneity was noticed.

Immunological microenvironment in prostate cancer: high mast cell densities are associated with favorable tumor characteristics and good prognosis

BACKGROUND

Number of intratumoral mast cells predicts survival in various cancers. The prognostic significance of such mast cells in surgically treated prostate cancer is unknown.

METHODS

Mast cell densities were determined in prostate cancer samples of more than 2,300 hormone-naïve patients using a tissue microarray format in correlation with clinical follow-up data. Mast cells were visualized immunohistochemically (c-kit). All patients were homogeneously treated by radical prostatectomy at a single institution.

RESULTS

Mast cells were present in 95.9% of the tumor samples. Median mast cell number on the tissue spot was 9 (range: 0-90; median density: 31 mast cells/mm(2)). High mast cell densities were significantly associated with more favorable tumors having lower preoperative prostate-specific antigen (P = 0.0021), Gleason score (P < 0.0001) and tumor stage (P < 0.0001) than tumors with low mast cell densities. Prostate-specific antigen recurrence-free survival significantly (P = 0.0001) decreased with decline of mast cell density showing poorest outcome for patients without intratumoral mast cells. In multivariate analysis mast cell density narrowly missed to add independent prognostic information (P = 0.0815) for prostate-specific antigen recurrence.

CONCLUSION

High intratumoral mast cell density is associated with favorable tumor characteristics and good prognosis in prostate cancer. This finding is consistent with a role of mast cells in the immunological host-defense reaction on prostate cancer. Triggering mast cell activity might expand immunotherapeutic strategies in prostate cancer.

Virtual microscopy and grid-enabled decision support for large-scale analysis of imaged pathology specimens

Breast cancer accounts for about 30% of all cancers and 15% of cancer deaths in women. Advances in computer-assisted analysis hold promise for classifying subtypes of disease and improving prognostic accuracy. We introduce a grid-enabled decision support system for performing automatic analysis of imaged breast tissue microarrays. To date, we have processed more than 1,00,000 digitized specimens (1200 x 1200 pixels each) on IBM's World Community Grid (WCG). As a part of the Help Defeat Cancer (HDC) project, we have analyzed that the data returned from WCG along with retrospective patient clinical profiles for a subset of 3744 breast tissue samples, and have reported the results in this paper. Texture-based features were extracted from the digitized specimens, and isometric feature mapping was applied to achieve nonlinear dimension reduction. Iterative prototyping and testing were performed to classify several major subtypes of breast cancer. Overall, the most reliable approach was gentle AdaBoost using an eight-node classification and regression tree as the weak learner. Using the proposed algorithm, a binary classification accuracy of 89% and the multiclass accuracy of 80% were achieved. Throughout the course of the experiments, only 30% of the dataset was used for training.

Quality aspects of the tissue microarray technique in a population-based cohort with ductal carcinoma in situ of the breast

AIMS

Tissue microarray (TMA) is an efficient technique for analysis of molecular markers. Prospectively collected samples have been reported to give excellent concordance between TMA data and corresponding whole-sections. The aim was to evaluate the usefulness of TMA in a population-based cohort of 213 women with ductal carcinoma in situ of the breast (DCIS).

METHODS AND RESULTS

We studied immunohistochemical HER2, oestrogen (ER) and progesterone (PR) receptor status. The prognostic impact was similar for all markers comparing whole sections and TMAs. The proportion of positive tumours was similar regarding HER2 and ER, whereas PR tumours were more frequently positive in the TMAs (P = 0.007). The concordance was 80% (kappa value 0.63) between original sections and TMAs. The proportion of successfully analysed tumours was 70%. Smaller tumours had a lower ratio (P < 0.0001) and a larger proportion of mismatched results (P = 0.05).

CONCLUSIONS

Retrospective analyses of tumours from cohorts with long-term follow-up are indispensable. We have shown that the TMA technique is a useful tool for high-throughput analysis of DCIS. However, our study has pinpointed some technical hazards within a population-based cohort, including many small lesions and the poor condition of some donor blocks. Mismatched results may be due to tumour heterogeneity.

Frequent expression of the novel cancer testis antigen MAGE-C2/CT-10 in hepatocellular carcinoma

Cancer testis (CT) antigens are attractive targets for immunotherapy in cancer patients. Immunohistochemistry was used to study the expression of the CT antigens MAGE-C2/CT-10, MAGE-C1/CT-7, GAGE, MAGE-A4 and NY-ESO-1 in 146 hepatocellular carcinomas, 13 intrahepatic cholangiocarcinomas, 37 extrahepatic cholangiocarcinomas and 32 gallbladder carcinomas. Immunopositivity was correlated with clinicopathological parameters, MHC Class 1 expression, intratumoral CD4+, CD8+ and FOXP3+ T cells and CD163+ antigen-presenting cells. Of the 146 hepatocellular carcinomas, 34% were positive for MAGE-C2/CT-10, 12% for MAGE-C1/CT-7, 11% for GAGE and 2% for NY-ESO-1, respectively. MHC Class 1 coexpression was identified in almost all CT antigen-positive tumors. The number of intratumoral FOXP3+ regulatory T cells was increased in CT antigen-positive hepatocellular carcinomas (p<0.004), suggesting inhibition of immune response in such tumors. Furthermore, MAGE-C1/CT-7 and GAGE positivity was correlated with reduced overall survival in patients with hepatocellular carcinoma (p=0.03 and 0.01, respectively). Four (13%) gallbladder carcinomas stained positive for MAGE-C2/CT-10, of which 1 tumor (3%) was also positive for NY-ESO-1 and GAGE. CT antigens were not expressed in intra- and extrahepatic cholangiocarcinomas. Our results suggest that MAGE-C2/CT-10 may be a good candidate for peptide vaccination in patients with hepatocellular carcinoma.

Prognostic marker profile to assess risk in stage I-III hormone receptor-positive breast cancer patients

Single markers are insufficient to accurately assess risk of relapse for adjuvant therapy guidance in operable breast cancer patients. In addition, the accuracy and interpretability of current multi-marker tests is generally limited by their simply additive algorithms and their overlap with clinicopathologic risks. Here, we report the development and validation of a nonlinear algorithm that combines protein (ER, PGR, ERBB2, BCL2 and TP53) and genomic (MYC/8q24) markers with standard clinicopathologic features (tumor size, tumor grade and nodal status) into a global risk assessment profile. The algorithm was trained using statistical pattern recognition in 200 stage I-III hormone receptor-positive patients treated with hormone therapy. Continuous risk scores (0-10+) were then generated for 232 independent patients. In hormone therapy-treated patients, the profile achieved a hazard ratio of 6.2 (95% confidence interval [CI], 1.8-20) in high- vs. low-risk groups for time to distant metastasis with the low-risk group having a 10-year metastasis rate of just 4% (95% CI, 0-8%). Similar results were achieved in untreated patients and for disease-specific survival. In multivariate analyses with standard prognostic factors and clinical practice guidelines, the profile was the only significant variable. Furthermore, the profile reclassified as low risk over half of node-negative patients at elevated risk according to the guidelines, which could have spared such patients from unnecessary cytotoxic chemotherapy. It also accurately identified a group of high-risk patients within a guideline low-risk group. In summary, the profile intelligently combines biologically relevant marker pathways and established clinicopathologic risks to help guide breast cancer patients to the most appropriate level of adjuvant therapy.

[Identification and validation of clinically relevant molecular alterations in prostate cancer]

Significant cellular alterations required for the development and progression of cancers are detectable at the molecular level and represent potential targets for gene-specific therapies. Modern chip techniques allow the parallel analysis of virtually all known human genes and proteins in a single experiment. Using modern high-throughput techniques, numerous potential new biomarkers for the diagnosis and prediction of prostate cancer have been identified. However, so far none of these markers has improved clinical practice. One of the most important challenges in the coming years is the extensive clinical validation of molecular data using clinically relevant end points. For this venture the pivotal prerequisite is the availability of large, comprehensively annotated and standardized high-quality bioresources.

Quantitative, fluorescence-based in-situ assessment of protein expression

As companion diagnostics grow in prevalence and importance, the need for accurate assessment of in situ protein concentrations has increased. Traditional immunohistochemistry (IHC), while valuable for assessment of context of expression, is less valuable for quantification. The lack of rigorous quantitative potential of traditional IHC led to our development of an immunofluorescence-based method now commercialized as the AQUA technology. Immunostaining of tissue samples, image acquisition, and use of AQUA software allow investigators to quickly, efficiently, and accurately measure levels of expression within user-defined subcellular or architectural compartments. IHC analyzed by AQUA shows high reproducibility and demonstrates protein measurement accuracy similar to ELISA assays. The process is largely automated, eliminating potential error, and the resultant scores are exported on a continuous scale. There are now numerous published examples where observations made with this technology are not seen by traditional methods.

[Identification and validation of clinically relevant molecular alterations in prostate cancer]

Significant cellular alterations required for the development and progression of cancers are detectable at the molecular level and represent potential targets for gene-specific therapies. Modern chip techniques allow the parallel analysis of virtually all known human genes and proteins in a single experiment. Using modern high-throughput techniques, numerous potential new biomarkers for the diagnosis and prediction of prostate cancer have been identified. However, so far none of these markers has improved clinical practice. One of the most important challenges in the coming years is the extensive clinical validation of molecular data using clinically relevant end points. For this venture the pivotal prerequisite is the availability of large, comprehensively annotated and standardized high-quality bioresources.

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.

Gene expression variation between distinct areas of breast cancer measured from paraffin-embedded tissue cores

Background

Diagnosis and prognosis in breast cancer are mainly based on histology and immunohistochemistry of formalin-fixed, paraffin-embedded (FFPE) material. Recently, gene expression analysis was shown to elucidate the biological variance between tumors and molecular markers were identified that led to new classification systems that provided better prognostic and predictive parameters. Archived FFPE samples represent an ideal source of tissue for translational research, as millions of tissue blocks exist from routine diagnostics and from clinical studies. These should be exploited to provide clinicians with more accurate prognostic and predictive information. Unfortunately, RNA derived from FFPE material is partially degraded and chemically modified and reliable gene expression measurement has only become successful after implementing novel and optimized procedures for RNA isolation, demodification and detection.

Methods

In this study we used tissue cylinders as known from the construction of tissue microarrays. RNA was isolated with a robust protocol recently developed for RNA derived from FFPE material. Gene expression was measured by quantitative reverse transcription PCR.

Results

Sixteen tissue blocks from 7 patients diagnosed with multiple histological subtypes of breast cancer were available for this study. After verification of appropriate localization, sufficient RNA yield and quality, 30 tissue cores were available for gene expression measurement on TaqMan^® Low Density Arrays (16 invasive ductal carcinoma (IDC), 8 ductal carcinoma in situ (DCIS) and 6 normal tissue), and 14 tissue cores were lost. Gene expression values were used to calculate scores representing the proliferation status (PRO), the estrogen receptor status and the HER2 status. The PRO scores measured from entire sections were similar to PRO scores determined from IDC tissue cores. Scores determined from normal tissue cores consistently revealed lower PRO scores than cores derived from IDC or DCIS of the same block or from different blocks of the same patient.

Conclusion

We have developed optimized protocols for RNA isolation from histologically distinct areas. RNA prepared from FFPE tissue cores is suitable for gene expression measurement by quantitative PCR. Distinct molecular scores could be determined from different cores of the same tumor specimen.

Clinical significance of p53 alterations in surgically treated prostate cancers

Despite the high number of previous studies, the role of p53 alterations in prostate cancer is not clearly defined. To address the role of p53 alterations in prostate cancer biology, a total of 2514 cancers treated by radical prostatectomy were successfully analyzed by immunohistochemistry in a tissue microarray format. Overall a low rate of p53-positive tumors was found (2.5%). A significant underestimation of p53-positive cases was excluded by subsequent large section analyses and direct sequencing of the p53 gene in subsets of our patients. Large section analysis of 23 cases considered negative on the tissue microarray yielded only one weakly p53-positive tumor. Only 4 out of 64 (6.4%) high-grade tumors, that were considered negative for p53 by immunohistochemistry, presented exon 5-8 mutations. These data suggest a high sensitivity of our immunohistochemistry approach and confirm the overall low frequency of p53 alterations in clinically localized prostate cancer. A positive p53 immunostaining was strongly associated with presence of exon 5-8 mutations (P<0.0001), advanced pT-stage (P<0.0001), high Gleason grade (P<0.0001), positive surgical margins (P=0.03) and early biochemical tumor recurrence (P<0.0001). A higher rate of positive p53 immunostaining was detected in late-stage diseases including metastatic prostate cancer (P=0.0152) and hormone-refractory tumors (P=0.0003). Moreover, p53 expression was identified as an independent predictor of biochemical tumor recurrence in the subgroup of low- and intermediate-grade cancers. In summary, the results of this study show that p53 mutations characterize a small biologically aggressive subgroup of prostate cancers with a high risk of progression after prostatectomy. The rate of p53 alterations increases with prostate cancer progression.

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.