Gene expression variation between distinct areas of XXXX measured from @entity982 -embedded tissue cores.

@entity1 @entity172 @entity3821 @entity0 @entity5 @entity406 @entity513 @entity982 @entity1722
BACKGROUND: Diagnosis and prognosis in @entity0 are mainly based on histology and immunohistochemistry of @entity406 -fixed, @entity982 -embedded (FFPE) material. Recently, gene expression analysis was shown to elucidate the biological variance between @entity5 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 @entity1 diagnosed with multiple histological subtypes of @entity0 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(R) Low Density Arrays (16 @entity513 ( @entity513 ), 8 @entity3821 ( @entity3821 ) and 6 normal tissue), and 14 tissue cores were lost. Gene expression values were used to calculate scores representing the proliferation status (PRO), the @entity172 receptor status and the @entity1722 status. The PRO scores measured from entire sections were similar to PRO scores determined from @entity513 tissue cores. Scores determined from normal tissue cores consistently revealed lower PRO scores than cores derived from @entity513 or @entity3821 of the same block or from different blocks of the same @entity1 . 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 @entity5 specimen.
