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(R) 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.

Paleoglaciated landscapes in Simen and other high-mountain areas of Ethiopia

In the present-day Ethiopia, glaciated landscapes do not exist, but paleoglaciated landscapes have been documented on a few mountain tops, which have altitudes higher than about 4,350 m asl in northern Ethiopia (Simen Mountains) and about 4,100 m asl in southern Ethiopia (Arsi and Bale Mountains). Glaciers were associated with the Late Pleistocene cold stages and reached as far down as 3,760 m asl in northern and 3,200 m asl in southern Ethiopia. Bale Mountains had the most extensive Late Pleistocene glaciation, covering over 190 km2, followed by Arsi Mountains (about 85 km2). In Simen, the Late Pleistocene glaciers covered merely 13 km2. In addition, paleo-periglacial slope deposits are found on all above-mentioned paleoglaciated mountains and in further mountain systems which did not host glaciers. This allows the reconstruction of the Late Pleistocene paleoclimate as being about 8 °C colder than at present (2014), much more dry, and probably without monsoon, at least in northern Ethiopia. Most probably in the Early Holocene, the re-emergence of monsoonal rains led to a strong erosion phase, which was followed by an extended stable phase with soil formation, building up about 70-cm-deep A-horizons (Andosol) on the paleo-periglacial slope deposits. These soils have been heavily degraded due to human-induced soil erosion up to about 3800 m asl since agriculture started several decades to millennia ago.