RNA quantitative analysis from fixed and paraffin-embedded tissues

Gene expression profiling from formalin-fixed paraffin-embedded tumors of pediatric glioblastoma

PURPOSE

Gene expression profiling has proved crucial for understanding the biology of cancer. In rare diseases, including pediatric glioblastoma (pGBM), the lack of readily available fresh frozen (FF) material limits the feasibility of this analysis, as well as its validation, on independent data sets, a step needed to ensure relevance, mandating the use of alternate RNA sources. To overcome the limitation of material number and to validate results we obtained on FF pGBM, we did microarray analysis on RNA extracted from formalin-fixed, paraffin-embedded archival samples from pGBM and control brains, wherein we had no control on the fixation process.

EXPERIMENTAL DESIGN

RNA from 16 pGBM and 3 control brains was extracted and linearly amplified. Reverse transcription-PCR on housekeeping and formerly identified tumor-associated genes and microarray analysis were done on this RNA source. Results were validated by immunohistochemistry.

RESULTS

Despite extensive RNA degradation, microarray analysis was possible on 16 of 19 samples and reproduced the pattern of results obtained on FF pGBM. Gene lists and ontology subgrouping were highly concordant in both sample types. Similar to the findings on FF samples, we were able to identify two subsets of pGBM based on their association/lack of association with evidence consistent with an active Ras pathway.

CONCLUSIONS

Archival formalin-fixed, paraffin-embedded tissues are an invaluable resource as they are the most widely available materials often accessible in conjunction with clinical and follow-up data. Gene expression profiling on this material is feasible and may represent a significant advance for understanding the biology of rare human diseases.

Insulin-like growth factor system gene expression in women with type 2 diabetes and breast cancer

BACKGROUND/AIMS

A twofold increased risk for breast cancer has been reported recently for women with late onset diabetes. Most studies showed that there were differences in serum concentrations of insulin-like growth factors and related proteins between women with and without diabetes who have breast cancer. This study investigated the expression of these markers at the cellular level in a cohort of women with and without type 2 diabetes who underwent biopsy because of a breast lump.

METHODS

Relative quantitative analysis of specific mRNA sequences was performed after extraction and reverse transcription polymerase chain reaction amplification from formalin fixed and paraffin wax embedded tissues. Sixty seven breast surgical specimens from women with and without diabetes who did not have cancer and from women with and without diabetes who did have cancer were studied for insulin-like growth factor I (IGF-I), the IGF-I receptor (IGF-IR), insulin-like growth factor binding protein 3 (IGFBP-3), and oestrogen receptor 1 gene expression.

RESULTS

The expression of IGF-I and IGF-IR was significantly lower in the cancer groups, whereas there was no significant difference for IGFBP-3 between women with and without cancer. Moreover, there was a good correlation between the expression of IGF-I and IGF-IR in women without cancer: this link was still present in breast tissue from patients with diabetes and cancer, whereas it was lost in patients without diabetes but with cancer.

CONCLUSIONS

These differences in IGF-I/IGF-IR expression could contribute to the increased risk for breast cancer in women with type 2 diabetes.

Molecular analyses of sentinel lymph nodes: an open question

AIMS

To detect micrometastases in the sentinel lymph nodes (SLN) of melanoma patients the authors analysed 52 lymph nodes (47 SLNs and five non-sentinel) and 17 corresponding primary skin melanomas using reverse transcriptase-polymerase chain reaction assays in paraffin-embedded tissues to detect the mRNAs of tyrosinase, MAGE1, MAGE3, MIA, MART-1 and mRNA coding for telomerase catalytic component.

RESULTS

Our data show that the use of molecular markers for melanoma micrometastases detection in SLN is still in a very preliminary stage. In comparing the molecular analysis results with the pathological staging we did not find any evident correlation with the expression of the analysed genes in SLN. There are no data for judging the prognostic significance of the detection of circulating tumour cells in patients without clinically recognizable metastases. Despite progress in the field with simultaneous detection of several markers it was assumed that tyrosinase mRNA remains the best target for the detection of metastatic melanoma cells.

Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction

Analysis of gene expression and correlation with clinical parameters has the potential to become an important factor in therapeutic decision making. The ability to analyze gene expression in archived tissues, for which clinical followup is already available, will greatly facilitate research in this area. A major obstacle to this approach, however, has been the uncertainty about whether gene expression analyses from routinely archived tissues accurately reflect expression before fixation. In the present study we have optimized the RNA isolation and reverse transcription steps for quantitative reverse transcription-polymerase chain reaction (RT-PCR) on archival material. Using tissue taken directly from the operating room, mRNAs with half-lives from 10 minutes to >8 hours were isolated and reverse transcribed. Subsequent real-time quantitative PCR methodology (TaqMan) on these cDNAs gives a measurement of gene expression in the fixed tissues comparable to that in the fresh tissue. In addition, we simulated routine pathology handling and demonstrate that this method of mRNA quantitation is insensitive to pre-fixation times (time from excision to fixation) of up to 12 hours. Therefore, it should be feasible to analyze gene expression in archived tissues where tissue collection procedures are largely unknown.

Correlation of MTS1/p16 and nm23 mRNA expression with survival in patients with peripheral synovial sarcoma

BACKGROUND AND OBJECTIVES

Tumor suppressor gene MTS1/p16 (cyclin-dependent kinase-4 inhibitor) and a putative tumor metastasis suppressor gene nm23 (nucleoside diphosphate A kinase) have been identified in a variety of human tumors but have not been well studied in mesenchymal neoplasms.

METHODS

Expression of nm23 and MTS1 mRNA was determined by quantitative analysis from paraffin-embedded tumor tissue. The series comprised 31 patients with localized primary synovial sarcoma of soft tissues who were followed for a median of 83 months.

RESULTS

Neither MTS1 nor nm23 expression levels correlated with the patient's age or sex, tumor type, depth, size, mitotic rate, or extent of tumor necrosis. In addition, there was no correlation between MTS1 and nm23 levels. Patients' survival was not related to sex, age, tumor type, location, mitotic rate, or MTS1 mRNA level. The only factors that correlated with poor survival in multivariate analysis were the presence of extensive tumor necrosis (> 15%) and higher levels of nm23 mRNA.

CONCLUSIONS

Our results suggest that increased expression level of nm23 mRNA may be implicated in the mechanism of tumor progression and is associated with poor survival in patients with synovial sarcoma.