Multiple use of slab gels in sequencing apparatus for separation of polymerase chain reaction products

Morphologically similar epithelial and stromal cells in primary bilateral breast tumors display different genetic profiles: implications for treatment

The morphologic features of primary bilateral breast carcinoma have been well elucidated, but it is not known whether tumors at two sides share a common genetic profile and undergo the same clinical course. To address this issue, morphologically comparable epithelial and stromal cells in 18 paired primary bilateral breast tumors were microdissected and subjected to comparisons for the frequency and pattern of loss of heterozygosity (LOH) and microsatellite instability (MI), as well as the profiles of comparative genomic hybridization. Of 18 paired bilateral epithelial samples assessed with 10 DNA markers at five chromosomes, 78 altered loci were found; of these, 23 (29.5%) displayed concurrent and 55 (70.5%) showed independent LOH, MI, or both. Of 18 paired bilateral stromal samples assessed with the same markers, 70 altered loci were seen; of these, 9 (12.9%) displayed concurrent and 61 (87.1%) showed independent LOH, MI, or both. Collectively, all the markers and 30 (83.3%) of 36 paired bilateral epithelial and stromal cells displayed significantly more (P < 0.01) independent than concurrent LOH, MI, or both. In contrast, the epithelial cells of a pulmonary small cell carcinoma metastasized to both breasts displayed concurrent LOH at each of the four altered loci. Of seven selected cases for comparative genomic hybridization, six (86%) displayed chromosomal changes, but none showed an identical pattern and frequency of changes in both breasts. The significantly higher rate of independent genetic alterations in morphologically comparable cells of paired bilateral primary breast tumors supports the notion that the development and clinical course of tumors in two sides differ substantially; consequently, different interventions might be needed for the optimal management of bilateral breast tumors.

Direct and repeat uses of tissue sections as templates for liquid-phase polymerase chain reaction amplification: applications and implications

The liquid-phase polymerase chain reaction (PCR) technique is the most commonly used method for the amplification of genetic materials, although it requires the lysis of cells for DNA or RNA extraction, making it impossible to visualize the distribution and subcellular localization of the biomolecules. This study intended to assess whether tissue sections may be directly and repeatedly used as templates for liquid-phase PCR amplifications. Consecutive paraffin sections of breast tissues were placed on gamma-methacryloxypropyltrimethoxysilane-coated microscopic cover glasses perforated with a diamond knife into strips. After hematoxylin and eosin or immuno-staining, the strip of interest was inserted into a PCR tube for amplifications, and the adjacent strip with the same tissue was subject to microdissection, DNA extraction, and PCR amplifications. To use the strip repeatedly, it was transferred into a new PCR tube and amplified with a new primer set, after an initial amplification for 5 to 7 cycles. Then, initially amplified samples were amplified to a total of 40 cycles. An equal volume of PCR products from the strip and DNA extract were loaded side by side for electrophoresis and detection. The strip and DNA extract from the same tissue yielded a very comparable quality and quantity of PCR products with the same primer sets. The strip, however, could be repeatedly used for PCR amplifications with substantially more primer sets. In addition, the strip could be used for immunohistochemical or other molecular assays after PCR amplifications. Further studies with the same protocol on strips containing chromosomal spreads generated similar results.

Cell clusters overlying focally disrupted mammary myoepithelial cell layers and adjacent cells within the same duct display different immunohistochemical and genetic features: implications for tumor progression and invasion

INTRODUCTION

Our previous studies detected focal disruptions in myoepithelial cell layers of several ducts with carcinoma in situ. The cell cluster overlying each of the myoepithelial disruptions showed a marked reduction in or a total loss of immunoreactivity for the estrogen receptor (ER). This is in contrast to the adjacent cells within the same duct, which were strongly immunoreactive for the ER. The current study attempts to confirm and expand previous observations on a larger scale.

METHODS

Paraffin sections from 220 patients with ER-positive intraductal breast tumors were double immunostained with the same protocol previously used. Cross-sections of ducts lined by > or = 40 epithelial cells were examined for myoepithelial cell layer disruptions and for ER expression. In five selected cases, ER-negative cells overlying the disrupted myoepithelial cell layer and adjacent ER-positive cells within the same duct were separately microdissected and assessed for loss of heterozygosity and microsatellite instability.

RESULTS

Of the 220 cases with 5698 duct cross-sections examined, 94 showed disrupted myoepithelial cell layers with 405 focal disruptions. Of the 94 cases, 79 (84%) contained only ER-negative cell clusters, nine (9.6%) contained both ER-negative and ER-positive cell clusters, and six (6.4%) contained only ER-positive cell clusters overlying disrupted myoepithelial cell layers. Of the 405 disruptions, 350 (86.4%) were overlain by ER-negative cell clusters and 55 (13.6%) were overlain by ER-positive cell clusters (P < 0.01). Microdissected ER-negative and ER-positive cells within the same duct from all five selected cases displayed a different frequency or pattern of loss of heterozygosity and/or microsatellite instability at 10 of the 15 DNA markers.

CONCLUSIONS

Cells overlying focally disrupted myoepithelial layers and their adjacent counterparts within the same duct displayed different immunohistochemical and molecular features. These features potentially represent an early sign of the formation of a biologically more aggressive cell clone and the myoepithelial cell layer breakdown possibly associated with tumor progression or invasion.

An Antigen Unmasking Protocol that Satisfies both Immunohistochemistry and Subsequent PCR Amplification

Immunohistochemical elucidation of many proteins in formalin-fixed, paraffin-embedded tissues requires a prior antigen unmasking treatment, which often damages both the morphology and genetic materials, making subsequent assessments difficult or impossible. This study attempted to develop a method that satisfies both immunohistochemical and genetic analyses. Consecutive sections were made from formalin-fixed, paraffin-embedded breast and other tissues, and a set of four adjacent sections from each case were treated with (1) routine H & E staining; (2) our unmasking protocol; (3) microwave oven irradiation; (4) pressure cooker incubation. After immunohistochemical staining, the tissue in each section was scraped off, or the same cell clusters in four sections were separately microdissected for DNA extraction and PCR amplification. Compared to microwave and pressure cooker methods, our protocol showed the following advantages: (1) a better preservation of the morphology; (2) a substantial reduction of tissue detachments from slides; (3) effectiveness on all antibodies tested, including those requiring enzyme digestion or no prior unmasking; (4) higher PCR yields; (5) larger (higher molecular weight) amplified PCR products. Compared to the routine method on untreated tissues, our method consistently produced a comparable quality and quantity of PCR products. Our protocol, however, takes a longer time to yield results.

An improved method for DNA extraction from paraffin sections

The acquisition of comparable quality and quantity of DNA extracts is the prerequisite to the success of comparative genetic analyses. Although several DNA extracting protocols on paraffin sections have been introduced, the importance of deparaffinization, the procedure for obtaining an adequate hematoxylin staining, the significance of the ratio of the cell number to the enzyme volume, and a practical means for monitoring the digestion process have not been sufficiently addressed. These, however, are the most important factors accountable for a failure of DNA extraction. To minimize the impact of these factors, we have developed several unique strategies, including: (1) incubating sections at 80 degrees C for 30-60 minutes prior to xylene treatment, (2) checking each section to insure the complete removal of paraffin; (3) treating hematoxylin stained sections or cells with de-staining solutions; (4) using a micrometer inserted into the eyepiece of a microscope to estimate the number of cells collected and adjusting the enzyme volume according to the cell number; and (5) monitoring the digestion process with a magnifier. With these strategies, we have been able to consistently obtain comparable quality and quantity of DNA extracts which yielded uniform PCR products regardless of variations in tissue embedding and processing.

Allelic losses at 3p and 11p are detected in both epithelial and stromal components of cervical small-cell neuroendocrine carcinoma

Microdissected epithelial and stromal cells from 15 cervical small-cell carcinoma patients and 9 healthy control subjects were assessed for loss of heterozygosity with polymorphic DNA markers at chromosomes 3p and 11p. Among malignant lesions assessed with 7 markers at 3p, 21 allelic losses were detected from 193 informative samples. Of losses, 20 were in epithelial and 1 was in normal-appearing stromal cells. Among losses in epithelial cells, 16 were from 44 samples informative for 3 markers within 3p21.2-p14.2 (0.36 loss/sample), whereas only 4 were from 54 samples informative for 4 markers outside the region (0.09 loss/sample), suggesting a "hot spot" of genetic alterations within 3p21.2-p14.2. Among malignant lesions assessed with 2 markers within 11p14-p12, 15 losses were seen in 52 informative samples. Of losses, 10 were in epithelial and 5 were in normal-appearing stromal cells. Of 10 epithelial samples showing losses within 11p14-p12, 8 also displayed losses within 3p21.2-p14.2, suggesting a concurrent involvement of these loci in tumor development or progression. The five losses in stromal cells were in four cases that showed no loss in epithelial cells with same markers, suggesting that stromal cells might play initiative roles in tumor development.