Cell blocks from scraping of cytology smear: comparison with conventional cell block

OBJECTIVE: To compare cytomorphology preservation and immunohistochemistry results between conventional cell blocks (CCB) and cytoscrape cell blocks (SCB). STUDY DESIGN: Fine needle aspiration (FNAC) was done in 17 consecutive cases. Air-dried smears for May-Grünwald-Giemsa stain and wet-fixed smear for hematoxylin-eosin (H-E) stain were prepared. Simultaneously another pass was made in each case for preparation of material for CCB. One of the H-E-stained smears was spared for SCB. SCB was compared with CCB for cell morphology. Immunostaining was performed both cell blocks, as well as on FNA smears in 8 cases. Results were evaluated for intensity of staining and percentage of cells showing positivity. RESULTS: CCB and SCB sections showed adequate cellularity in all cases. Morphologic preservation was good in SCB sections. There was good architectural and nuclear preservation in all cases of SCB. Immunostaining results showed better and clear intensity of staining with little background in all cell block cases. CONCLUSION: SCB is a valuable technique in cell blocks from stained FNA smears. The cytomorphologic details are equally good in SCB and CCB. Additional panels of immunostaining can be done on SCB for better diagnosis and classification, particularly in cases in which repeat FNA is not possible.     

A new convenient technique for making cell blocks

Cell block sections serve as an important diagnostic annex for cytological smears, liquid-based SurePath cytology and the Liquid-based Thin-prep Cytology Test (TCT). A variety of methods for the preparation of cell blocks are described in the literature and the techniques in cell blocks are in continuous improvement. A new technique for making cell blocks was introduced in the present study. We first used pregelatinized starch as the frame for the cell block, which is a really simple and economic method, because it can be carried out at room temperature without additional special instruments. We have performed hematoxylin and eosin (HE) staining, immunohistochemistry analysis and fluorescence in situ hybridization (FISH) in the cell block sections in 122 cytological specimens. The results demonstrated in this article show that pregelatinized starch is a useful frame for cell blocks. The pregelatinized starch can effectively collect even a few cells with powerful adhesiveness. Therefore, this new technique for making cell blocks is especially useful for cytologic samples with low cellularity, such as cerebrospinal fluid specimens.     

A technique for section thickness evaluation for microphotometry and image analysis of sectioned nuclei.

The exact knowledge of the section thickness is a requisite for making the necessary corrections on DNA measurements in tissue sections. Several methods have been proposed to evaluate section thickness, each of them with advantages and disadvantages depending on the type of specimen and equipment available. We herein report another method based on preparation of standard material whose optical density varies as a function of its thickness and is sectioned and measured alongside the tissue specimen. The standards consist of celloidin cylinders stained with the PAS reaction and embedded in paraffin. For prior characterization of the cylinders, sections of different thickness were obtained and mounted. The optical density of each section was measured by direct microphotometry or image analysis. The actual thickness of each section was evaluated following re-embedding of piled groups of sections in a paraffin block and transversal sectioning. The thickness was then measured with a micrometric eye-piece. Optical density and actual thickness of each section were plotted on a normogram curve. Once a given tissue is sectioned alongside with the reference cylinder, the actual thickness is determined by its optical density on the normogram curve.     

An automatic block and spot indexing with k-nearest neighbors graph for microarray image analysis

MOTIVATION: In this paper, we propose a fully automatic block and spot indexing algorithm for microarray image analysis. A microarray is a device which enables a parallel experiment of ten to hundreds of thousands of test genes in order to measure gene expression. Due to this huge size of experimental data, automated image analysis is gaining importance in microarray image processing systems. Currently, most of the automated microarray image processing systems require manual block indexing and, in some cases, spot indexing. If the microarray image is large and contains a lot of noise, it is very troublesome work. In this paper, we show it is possible to locate the addresses of blocks and spots by applying the Nearest Neighbors Graph Model. Also, we propose an analytic model for the feasibility of block addressing. Our analytic model is validated by a large body of experimental results. RESULTS: We demonstrate the features of automatic block detection, automatic spot addressing, and correction of the distortion and skewedness of each microarray image.     

Chondrosarcoma of the spine: A rare case with unusual presentation

Background

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

Methods

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

Results

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

Conclusion

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

Classification of DNA methylation patterns in tumor cell genomes using a CpG island microarray

Our group has initiated experiments to epigenetically profile CpG island hypermethylation in genomic DNA from tissue specimens of head and neck squamous cell carcinoma (HNSCC) using a microarray of 12,288 CpG island clones. Our technique, known as a methylation-specific restriction enzyme (MSRE) analysis, is a variation of the differential methylation hybridization (DMH) technique, in that it is not an array comparison of two DNA samples using methylation-specific restriction enzymes. Instead, it is a comparison of a single DNA sample's response to a methylation-sensitive restriction enzyme (HpaII) and its corresponding methylation-insensitive isoschizomer (MspI). Estimation of the reproducibility of this microarray assay by intraclass correlation (ICC) demonstrated that in four replicate experiments for three tumor specimens, the ICC observed for a given tumor specimen ranged from 0.68 to 0.85 without filtering of data. Repeated assays achieved 87% concordance or greater for all tumors after filtering of array data by fluorescence intensity. We utilized hierarchical clustering on a population of 37 HNSCC samples to cluster tumor samples with similar DNA methylation profiles. Supervised learning techniques are now being utilized to allow us to identify associations between specific epigenetic signatures and clinical parameters. Such techniques will allow us to identify select groups of CpG island loci that could be used as epigenetic markers for both diagnosis and prognosis in HNSCC.     

Discrepancies in ploidy determination due to specimen sampling errors

Two techniques are described to enhance the detection of low frequency aneuploid cells in automated cell analysis. One method concerns a cell preparation technique; the other is focused on specific cell selection at the measurement level. The cell preparation method has been designed to select and process the tumour areas in paraffin blocks and can be used for image as well as for flow cytometry. The technique uses incident fluorescence microscopy for visual inspection of the surface of the fluorescently stained tissue block to select the specific tumour parts. Using image cytometry, it is shown that in tissue sections with very small tumour foci and many normal cells, aneuploidy could only be detected after enrichment of the cell sample with the specifically selected areas. The cell selection at the measurement level is directed towards detection of low frequency aneuploid cells on microscope slides using the specific capacities of LEYTAS (Leyden Television Analysis System). With this system, cells of interest can be selected by means of minimum size and intensity thresholds. In addition to measurement of the total cell population, all cells above a minimum DNA value can thus be specifically selected and measured. The advantage of both enrichment techniques is the possibility to detect and measure aneuploid cell lines in cases where normal, diploid cells dominate the paraffin tissue.     

A novel cell array technique for high-throughput,cell-based analysis

Summary Microarray technology has burgeoned over the past few years from nucleic acid-based arrays to tissue microarrays (TMAs). This study aimed to develop a technique to incorporate cell lines into an array and to demonstrate the usefulness of this technique by performing immunohistochemistry for β-catenin. Cell suspensions were prepared from 23 tumor cell lines. These were fixed in formalin, suspended in agar, and embedded in paraffin to produce a cell block. A “tissue microarrayer” was used to remove triplicate, 0.6 mm-cores from each cell block and to transfer these into a recipient paraffin block at precise coordinates. Immunohistochemistry was used to identify cell lines positive for β-catenin. Cultured cells were successfully incorporated into the microarray, with preservation of cell architecture and even distribution of cells within each core. A total of 18 of 69 cores (26%) were lost in processing. A total of 16 of 23 cell lines were identified as positive for membrane and cytoplasmic β-catenin, and 6 of 23 were negative. Only one cell line was unscorable because of complete core loss. We have developed a “cell microarray” technique for analyzing antigen expression by immunohistochemistry in multiple cell lines in a single expriment. This novel application of microarrays permits high-throughput, cost-efficient analysis, with the potential to rapidly identify markers with potential diagnostic and therapeutic implications in human disease.     

Double Embedding Broad Thin Leaves in Paraffin

Paraffin pellets were melted in 24 × 24 × 5 mm stainless steel base molds. Specimens of leaves, 18 × 18 mm, were fixed, dehydrated and infiltrated with paraffin. Two specimens were transferred into molten paraffin on their laminar surfaces in a base mold and moved quickly onto a cold surface to cast them in a shallow block of paraffin. Each block was then scored with a razor blade, broken into two primary blocks, and trimmed to 20 × 9 mm with 5 mm flat edges. Each primary block was immersed upright on its long edge in a 22 × 22 × 20 mm Peel-A-Way® embedding mold containing molten paraffin. The leaf edge was held centrally in the mold while moving the double embedment onto a cold surface. In this secondary block, the leaf specimen stood perpendicular to the sectioning surface in perfect orientation for transverse ribbon sectioning. The two phases of paraffin bonded well.     

Immunocytochemistry on scrape cytology in breast cancer: will it unearth the weaker positives?

OBJECTIVE: To standardize the technique of immunocytochemical (ICC) assessment of estrogen (ER) and progesterone receptor (PR) status in breast cancer by scrape cytology and to compare the results with immunohistochemistry on paraffin blocks. STUDY DESIGN: ICC assessment for ER and PR was done on scrape smears from tissue samples in 200 cases of primary breast cancer. The results were compared to those obtained from immunohistochemical (IHC) evaluation of formalin-fixed paraffin same tissue samples. RESULTS: ER/PR positivity rates as well as staining scores were compared between the scrape smears and tissue sections. The concordance between cytology and histology was 84% for ER and 90% for PR. Both the positivity rates and the staining intensity scores were higher for cytochemistry than for histochemistry. CONCLUSION: The ICC method on scrape smears is a simple test with rapid turnaround time. The sample required is small, and antigen loss due to fixation and processing is minimal. This new method gives a higher yield of hormone receptor positivity and, when used in conjunction with the IHC method, may improve the pickup rate of ER-positive cases, thereby playing an important role in risk stratification and therapeutic decision making in patients with breast cancer.     

External quality control for immunocytochemistry on cytology samples: a review of UK NEQAS ICC (cytology module) results

I. S. Kirbis, P. Maxwell, M. S. Fle?ar, K. Miller and M. Ibrahim External quality control for immunocytochemistry on cytology samples: a review of UK NEQAS ICC (cytology module) results Objective: To date, external quality control for immunocytochemistry on cytology samples is provided only by the United Kingdom national external quality assessment service for immunocytochemistry and in situ hybridisation (UK NEQAS ICC & ISH). For the purpose of this study a retrospective analysis of a comprehensive collection of quality‐related data regarding immunocytochemistry on cytology samples collected through this service was analysed. Methods: The quality of immunocytochemical reactions, using on‐line collected data, was analysed for the last 23 UK NEQAS ICC cytology module external quality assessments carried out on cytology samples completed in the period from 2004 to 2010. Results: Our study showed that the majority of participants in the cytology module (66%) sent formalin‐fixed paraffin‐embedded (FFPE) tissue sections for assessment as in‐house control slides and only 34% sent cytology slides of various types. The highest UK NEQAS ICC score for the quality of immunocytochemical staining among in‐house control slides was achieved on cell block sections, followed by cytospins, FFPE tissue sections, liquid‐based cytology slides and smears. With regard to fixation, acetone‐fixed slides achieved significantly lower scores than other reported fixatives. The strength of agreement in perception of immunocytochemical staining quality was good between in‐house assessors (Kappa = 0.64) but only fair between in‐house and UK NEQAS ICC assessors (Kappa = 0.22). Conclusions: Good quality of immunocytochemical staining can be achieved on cytology slides prepared and fixed in different ways as well as on cell blocks. Unified criteria for high‐quality immunocytochemical staining and proper internal and external quality assurance could facilitate further improvement and standardization of immunocytochemistry on cytology samples.     

Significance of pericellular lacunae in cell blocks of effusions.

A retrospective study was conducted to assess the usefulness of pericellular lacunae in cell block sections of serous effusions in diagnosis. From January to December 1988, 286 cell blocks were prepared in our laboratory from pleural, pericardial and peritoneal fluids; 62 of them were excluded from this study because of inadequate cellularity, diagnostic uncertainty or lack of a proteinaceous background. The remaining consisted of 148 benign effusions from 128 patients and 76 malignant effusions from 56 patients. A single specimen from each patient was selected and reviewed to assess the presence and number of pericellular lacunae and to determine the relationship of this feature to cell arrangement (single cells versus cell clusters). Pericellular lacunae were found in 42 (75%) of the malignant effusions as compared to 41 (32%) of benign specimens. In the majority of malignant cases with lacunae, this feature was associated with greater than two-thirds of the cells, whereas in benign cases, when present, it was seen in less than one-third of the cells. Neoplasms characterized by large cell clusters more frequently had lacunae than did those with small groups or single cells. Lacunae were not evident in cases of malignant melanoma and lymphoma. We conclude that although pericellular lacunae are more often associated with malignant cells, their presence in itself cannot be used as a reliable indicator of malignancy in body cavity fluids.     

A novel tissue array technique for high-throughput tissue microarray analysis — microarray groups

Tissue microarrays are ordered arrays of hundreds to thousands of tissue cores in a single paraffin block. We invented a novel method to make a high-throughput microarray group. Conventional smaller tissue microarrays were made first and then sectioned. Separate paraffin films were arrayed orderly onto a regular-sized glass slide to form a larger microarray group. Sections were not floated in a water bath but, rather, were cut singly using conventional microtome, arrayed orderly onto the glass slide with forceps instead of using a tape-based tissue transfer system, and then unfolded with warm water (46° C) using a micropipette. This not only lowers the difficulty in sectioning but the overall tissue disks can be included in the same section. A microarray group of 2,534 small disks (theoretically, 2,560 disks can be made; 26 fell off during the procedure), the most up to now, was successfully made and may be used in immunohistochemistry, mRNA in situ hybridization, and flourescent in situ hybridization.     

Sputum cytology for the diagnosis of lung cancer. Comparison of smear and modified cell block methods

OBJECTIVE: To compare the sputum smear cytology and cell block methods for specimen adequacy, cytology quality and diagnostic accuracy in the diagnosis of lung cancer. STUDY DESIGN: We assessed 2,524 sputum specimens from 768 patients. The specimens were prepared as smears and cell blocks for cytopathologic examination between March 1, 1992, and December 31, 1998. The smear and cell block slides were evaluated both separately and together, and the results were compared with radiologic and histopathologic diagnoses. RESULTS: The sensitivity of the smear method was 69.4% and specificity was 99.5%. The sensitivity of the cell block method was 84.4% and specificity, 100%. The sensitivity of the smear and cell block together was 87.6% and specificity, 99.5%. CONCLUSION: The cell block method increases the sensitivity and specificity of sputum cytology, and when smear and cell block slides are evaluated together, sensitivity reaches its highest value. Therefore, application of smear and cell block methods together seems most useful in the diagnosis of lung cancer.     

Protective Paraffin Infiltration of Soft Tissues in Insects to Facilitate Softening of Hard Exoskeletons

This technique can produce serial sections as thin as 5 μ from hard chitin-covered materials of insects or other arthropods. Procedures: Fix with alcoholic Bouin's fluid for 3 hr. Henceforth subject material to partial vacuum in each step to ensure a final proper embedding. Wash with 80% ethanol 2 or 3 times for 2 hr or until the picric acid is largely removed. Dehydrate to 90% ethanol and give 2 changes of n-butanol 2 hr each, and one of a 1:1 n-butanol-paraffin mixture in 56-57° oven for 12 hr. Finally, use 2 baths of pure paraffin, 3 hr each, to complete the infiltration. After the last bath, withdraw the specimen from the paraffin, and remove the superficial paraffin, first mechanically and then with a xylene bath for 4 min. Rinse first with n-butanol, and afterwards with absolute ethanol, 2 min each. The compound eyes are protected with a paraffin covering, the specimen is hydrated with a 1% aqueous solution of detergent for 1 hr and then washed with running tap water. The material is treated with a concentrated sulfuric-nitric mixture (H₂SO₄:HNO₃) for 4 hr to eliminate the exoskeleton. After this treatment, the specimen is washed with running tap water for 12 hr, dehydrated with acetone and then bathed in a 2% solution of celloidin in ethyl acetate to form a protective artificial cuticle. This coating is hardened with 2 quick baths of chloroform, the specimen reembedded in paraffin, and the block cast for sectioning.     

Construction of a tissue microarray with two millimeters cores of endometrioid endometrial cancer: factors affecting the quality of the recipient block

The tissue microarray (TMA) method currently is not used to render a primary diagnosis of cancer, but its scientific value has been proved in studies of various cancer types. TMA technology still is not used often for uterine tumors, however. We investigated the repeatability of histological diagnosis of endometrioid endometrial cancer (EEC) using conventional histology and TMA using 2 mm cores. We examined EEC tissues from 171 patients. Formalin fixed, paraffin embedded tissue donor blocks from EEC specimens were selected and examined histologically. Duplicate 2 mm tissue cores were inserted into a TMA recipient block. EEC tissues were examined as hematoxylin-eosin stained sections from the TMAs. EEC tissue was identified in the TMAs in 158 cases (92.4%) and not found in 13 cases (7.6%). On the TMA slides, both EEC positive cores were identified in 129 cases (75.4%), but only one core in 29 cases (17.0%). Among 342 biopsies of the donor blocks (each case in duplicate), EEC was found in 287 cases (83.9%) using the TMA: 124/146 (84.9%) with superficial infiltration, 153/178 (86.0%) with deep myometrial infiltration, and 10/18 (55.6%) without myometrial infiltration. We concluded that two 2 mm tissue cores from a biopsy of a donor block inserted into a TMA recipient block were sufficient to diagnose EEC in more than 90% of cases. EEC was identified in the TMAs with similar frequency with respect to superficial and deep myometrial infiltration. Cases without myometrial infiltration were identified less often.     

Immunocytochemistry and fluorescence in situ hybridization in HER-2/neu status in cell block preparations

OBJECTIVE: Recent studies have validated the use of cytologic materials to determine HER-2/neu status. Good concordance has been shown between results obtained by immunocytochemistry (ICC), immunohistochemistry (IHC), fluorescence in situ hybridization (FISH) on cytologic and surgical specimens. However, the utility of cytologic cell block material in determining HER-2/neu status has not been reported and is the subject of this study. STUDY DESIGN: HER-2/neu status was determined in 25 cases of primary or metastatic breast carcinoma by IHC and FISH. All cases were formalin-fixed, paraffin-embedded (FPPE) cell block preparations. ICC was performed using monoclonal antibodies TAB250 (Zymed) and CB11 (Novacastra Laboratories). FISH analysis was performed using the PathVysion HER-2 probe kit (Vysis, Inc.). Results of ICC and FISH were compared in each case. RESULTS: Of 25 cases studied, 17 showed no protein overexpression or amplification. Five cases showed protein overexpression and amplification. The remaining 3 cases showed 2+ staining intensity by ICC in 10, 20, and 50% of carcinoma cells, respectively, and all demonstrated lack of amplification. CONCLUSION: Immunocytochemistry performed on FFPE cell block material is a reliable method for determining HER-2/neu status in cytologic specimens. We recommend routine preparation of FFPE cell block material in instances of suspected primary of metastatic breast carcinoma.     

Automatic registration of microarray images. I. Rectangular grid

MOTIVATION: The analysis of high-throughput experiment data provided by microarrays becomes increasingly more and more important part of modern biological science. Microarrays allow to conduct genotyping or gene expression experiments on hundreds of thousands of test genes in parallel. Because of the large and constantly growing amount of experimental data the necessity of efficiency, robustness and complete automation of microarray image analysis algorithms is gaining significant attention in the field of microarray processing. RESULTS: The author presents here an efficient and completely automatic image registration algorithm (that is an algorithm for spots and blocks indexing) that allows to process a wide variety of microarray slides with different parameters of grid and block spacing as well as spot sizes. The algorithm scales linearly with the grid size, the time complexity is O(M), where M is number of rows x number of columns. It can successfully cope with local and global distortions of the grid, such as focal distortions and non-orthogonal transformations. The algorithm has been tested both on CCD and scanned images and showed very good performance-the processing time of a single slide with 44 blocks of 200 x 200 grid points (or 1 760 000 grid points total) was about 10 s. AVAILABILITY: The test implementation of the algorithm will be available upon request for academics. Supplementary information: http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf     

miR-15a-5p和miR-16-5p在骨肉瘤组织中的表达分析

目的:使用microRNAs基因芯片及实时定量PCR法测定骨肉瘤组织中miR-15a-5p和miR-16-5p的相对表达含量,并与瘤旁组织对比,分析骨肉瘤细胞内miR-15a-5p和miR-16-5p的表达变化。方法:选取34例骨肉瘤组织蜡块样本,使用microRNAs基因芯片观察miR-15a-5p和miR-16-5p在骨肉瘤和瘤旁组织内的表达差异;实时定量PCR法测定骨肉瘤组织和瘤旁组织中miR-15a-5p和miR-16-5p的相对表达含量,并将两种结果对比分析。结果:microRNAs基因芯片结果显示,在骨肉瘤组织中,miR-15a-5p在肿瘤中的表达较瘤旁组织低1.79倍,miR-16-5p较瘤旁组织低1.62倍。实时定量PCR实验结果表明,miR-15a-5p和miR-16-5p表达较瘤旁组织降低,差异有统计学意义(P0.05)。经过统计学计算,miR-15a-5p在肿瘤中的表达较瘤旁组织低3.14倍,miR-16-5p较瘤旁组织低5.65倍。结论:在骨肉瘤中,miR-15a-5p和miR-16-5p表达含量降低,提示这两种microRNAs在骨肉瘤中可能做为抑癌因子存在。