Expression profiling with RNA from formalin-fixed, paraffin-embedded material

<p>Abstract</p> <p>Background</p> <p>Molecular characterization of breast and other cancers by gene expression profiling has corroborated existing classifications and revealed novel subtypes. Most profiling studies are based on fresh frozen (FF) tumor material which is available only for a limited number of samples while thousands of tumor samples exist as formalin-fixed, paraffin-embedded (FFPE) blocks. Unfortunately, RNA derived of FFPE material is fragmented and chemically modified impairing expression measurements by standard procedures. Robust protocols for isolation of RNA from FFPE material suitable for stable and reproducible measurement of gene expression (e.g. by quantitative reverse transcriptase PCR, QPCR) remain a major challenge.</p> <p>Results</p> <p>We present a simple procedure for RNA isolation from FFPE material of diagnostic samples. The RNA is suitable for expression measurement by QPCR when used in combination with an optimized cDNA synthesis protocol and TaqMan assays specific for short amplicons. The FFPE derived RNA was compared to intact RNA isolated from the same tumors. Preliminary scores were computed from genes related to the ER response, HER2 signaling and proliferation. Correlation coefficients between intact and partially fragmented RNA from FFPE material were 0.83 to 0.97.</p> <p>Conclusion</p> <p>We developed a simple and robust method for isolating RNA from FFPE material. The RNA can be used for gene expression profiling. Expression measurements from several genes can be combined to robust scores representing the hormonal or the proliferation status of the tumor.</p

Species-Area Relationships Are Controlled by Species Traits

The species-area relationship (SAR) is one of the most thoroughly investigated empirical relationships in ecology. Two theories have been proposed to explain SARs: classical island biogeography theory and niche theory. Classical island biogeography theory considers the processes of persistence, extinction, and colonization, whereas niche theory focuses on species requirements, such as habitat and resource use. Recent studies have called for the unification of these two theories to better explain the underlying mechanisms that generates SARs. In this context, species traits that can be related to each theory seem promising. Here we analyzed the SARs of butterfly and moth assemblages on islands differing in size and isolation. We tested whether species traits modify the SAR and the response to isolation. In addition to the expected overall effects on the area, traits related to each of the two theories increased the model fit, from 69% up to 90%. Steeper slopes have been shown to have a particularly higher sensitivity to area, which was indicated by species with restricted range (slope  = 0.82), narrow dietary niche (slope  = 0.59), low abundance (slope  = 0.52), and low reproductive potential (slope  = 0.51). We concluded that considering species traits by analyzing SARs yields considerable potential for unifying island biogeography theory and niche theory, and that the systematic and predictable effects observed when considering traits can help to guide conservation and management actions

Breast cancer and human papillomavirus (HPV) infection: No evidence of a viral etiology in a group of Swiss women

There are controversial data on the meaning of viral induction of breast cancer. The aim of this study was to investigate the presence of human papillomavirus (HPV) DNA in patients with breast carcinoma and the correlation of viral infection with disease outcome. Paraffin-embedded sections from 81 patients with breast cancer were analyzed for HPV DNA by polymerase chain reaction (PCR) using the SPF1/2 primers covering about 40 different low-, intermediate- and high-risk types. We found all samples were negative for HPV DNA. Our analysis could not support a role of HPV in breast carcinoma. Controversial published data indicate a need for further, larger epidemiologic studies

The odontogenic keratocyst--odontogenic cyst or benign tumor?

The odontogenic keratocyst is the third most common cyst of the jaws, after the follicular and radicular cyst. Keratocysts most commonly occur as single lesions in the jaw of otherwise healthy persons. Multiple odontogenic keratocysts are a well-recognized feature of the nevoid basal cell carcinoma syndrome. The mandible, especially the third molar region, the angle of the mandible and the ascending ramus are involved far more frequently than the maxilla. Clinically, the cysts often remain asymptomatic and there are two specific histological entities: the orthokeratinized and the parakeratinized odontogenic keratocyst. Different surgical treatment options like marsupialization, enucleation with curettage or peripheral ostectomy, and osseous resection (marginal or segmental) have been discussed in the literature with variable rates of recurrence. Besides a predilection for recurrence, the keratocysts, in contrast to other odontogenic cysts, show a more aggressive clinical behavior and demonstrate a high mitotic count and higher turnover rate of the epithelium. This led to the tentative suggestion that the keratocyst might be a benign cystic neoplasm rather than simply an odontogenic cyst.Link_to_subscribed_fulltex

The "globulomaxillary cyst" a specific entity or a myth?

The following review investigates the term and concept of the globulomaxillary cyst as a correct clinico-pathological diagnosis to describe a so-called fissural cyst said to be caused by epithelial entrapment between the nasal and maxillary process. After analyzing the available literature it has to be concluded that neither from an embryologic nor from a clinical or pathohistological standpoint the term globulomaxillary cyst represents a real entity by itself. Therefore, globulomaxillary cysts have to be diagnosed alternatively after a thorough clinical, radiological and histological examination as other odontogenic cysts like dentigerous cysts or odontogenic keratocysts, odontogenic tumors like ameloblastoma, central giant cell tumors, solitary bone cysts, etc.Link_to_subscribed_fulltex

[The "globulomaxillary cyst" a specific entity or a myth?]

The following review investigates the term and concept of the globulomaxillary cyst as a correct clinico-pathological diagnosis to describe a so-called fissural cyst said to be caused by epithelial entrapment between the nasal and maxillary process. After analyzing the available literature it has to be concluded that neither from an embryologic nor from a clinical or pathohistological standpoint the term globulomaxillary cyst represents a real entity by itself. Therefore, globulomaxillary cysts have to be diagnosed alternatively after a thorough clinical, radiological and histological examination as other odontogenic cysts like dentigerous cysts or odontogenic keratocysts, odontogenic tumors like ameloblastoma, central giant cell tumors, solitary bone cysts, etc

Impact of viral E2-gene status on outcome after radiotherapy for patients with human papillomavirus 16-positive cancer of the uterine cervix

PURPOSE: Integration of high-risk papillomavirus DNA has been considered an important step in oncogenic progression to cervical carcinoma. Disruption of the human papillomavirus (HPV) genome within the E2 gene is frequently a consequence. This study investigated the influence of episomal viral DNA on outcome in patients with advanced cervical cancer treated with primary radiotherapy. METHODS AND MATERIALS: Paraffin-embedded biopsies of 82 women with locally advanced cervical cancer could be analyzed for HPV infection by multiplex polymerase chain reaction (PCR) by use of SPF1/2 primers. E2-gene intactness of HPV-16-positive samples was analyzed in 3 separate amplification reactions by use of the E2A, E2B, E2C primers. Statistical analyses (Kaplan-Meier method; log-rank test) were performed for overall survival (OS), disease-free survival (DFS), local progression-free survival (LPFS), and distant metastases-free survival (DMFS). RESULTS: Sixty-one (75%) of 82 carcinomas were HPV positive, 44 of them for HPV-16 (72%). Seventeen of the 44 HPV-16-positive tumors (39%) had an intact E2 gene. Patients with a HPV-16-positive tumor and an intact E2 gene showed a trend for a better DFS (58% vs. 38%, p = 0.06) compared with those with a disrupted E2 gene. A nonsignificant difference occurred regarding OS (87% vs. 66%, p = 0.16) and DMFS (57% vs. 48%, p = 0.15). CONCLUSION: E2-gene status may be a promising new target, but more studies are required to elucidate the effect of the viral E2 gene on outcome after radiotherapy in HPV-positive tumors