Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Background

In Sweden, human tissue samples obtained from diagnostic and surgical procedures have for decades been routinely stored in a formalin-fixed, paraffin-embedded, form. Through linkage with nationwide registers, these samples are available for molecular studies to identify biomarkers predicting mortality even in slow-progressing prostate cancer. However, tissue fixation causes modifications of nucleic acids, making it challenging to extract high-quality nucleic acids from formalin fixated tissues.

Methods

In this study, the efficiency of five commercial nucleic acid extraction kits was compared on 30 prostate biopsies with normal histology, and the quantity and quality of the products were compared using spectrophotometry and Agilent’s BioAnalyzer. Student’s t-test’s and Bland-Altman analyses were performed in order to investigate differences in nucleic acid quantity and quality between the five kits. The best performing extraction kits were subsequently tested on an additional 84 prostate tumor tissues. A Spearman’s correlation test and linear regression analyses were performed in order to investigate the impact of tissue age and amount of tissue on nucleic acid quantity and quality.

Results

Nucleic acids extracted with RNeasy® FFPE and QIAamp® DNA FFPE Tissue kit had the highest quantity and quality, and was used for extraction from 84 tumor tissues. Nucleic acids were successfully extracted from all biopsies, and the amount of tumor (in millimeter) was found to have the strongest association with quantity and quality of nucleic acids.

Conclusions

To conclude, this study shows that the choice of nucleic acid extraction kit affects the quantity and quality of extracted products. Furthermore, we show that extraction of nucleic acids from archival formalin-fixed prostate biopsies is possible, allowing molecular studies to be performed on this valuable sample collection.

     

Mitochondrial cascade hypothesis of Alzheimer's disease: myth or reality?

Mitochondria are recognized to play a pivotal role in neuronal cell survival or death because they are regulators of both energy metabolism and apoptotic pathways. Morphologic, biochemical, and molecular genetic studies suggest that mitochondria might be a convergence point for neurodegeneration, including Alzheimer's disease (AD). The functions and properties of mitochondria might render subsets of selectively vulnerable neurons intrinsically susceptible to cellular aging and stress. However, the question, "Is mitochondrial dysfunction a necessary step in neurodegeneration?" is still unanswered. This review presents the ways in which malfunctioning mitochondria and oxidative stress might contribute to neuronal death in AD.     

Supracondylar humerus fractures in children treated with closed reduction and percutaneous pinning

Supracondylar fractures of the humerus in children are important for frequency and type of associated serious complications. The management of this kind of fractures is still controversial (Skaggs et al. in J Bone Joint Surg Am 86:702–707, 2004; Kalllio et al. in J Pediatr Orthop 12:11–15, 1992). We are going to present our experience in the treatment of supracondylar humeral fracture in children. In the Orthopedic Department of Pisa, we treated 150 cases from 1989 to 2006. We are used to perform, emergency or within 12 h, reduction and two lateral-entry percutaneous pins fixation. The mean age was 7.5 years. We checked 125 cases, because we excluded all the cases with follow up less then 5 years. The mean follow up was 8.2 years. We used Gartland classification modified by Wilkins. We evaluated 125 cases by using the Flynn classification: 100 % of patients did not have impairment of the elbow joint mobility. We had seven valgus deviation, one of which was more then 10°. We also had 17 varus deviations, 11 of which were not over 8° and only 2 of them were 15°. The average value of the joint Baumann angle was calculated as great as 16°. The obtained results were classified as very good 80 %, good 11 %, sufficiently good 6 %, and bad 3 %. In our experience, all the fractures type II and III by Gartland have to be treated within 12 h, with closed reduction and stabilization with lateral-entry K-wire technique. The conservative treatment by cast is indicated only in type I fracture. The trans olecranic treatment is not realizable, for the stiffness which can occur, for the risk of iatrogenic ulnar nerve lesion, and for long-time hospitalization. The open reduction remains the first choice treatment for exposed or nonreducible fractures, and in cases of vascular injury.     

Recurrent acute obstructive hydrocephalus as clinical onset of cerebral Whipple's disease

Whipple's disease is a rare multisystemic infection caused by the intracellular bacteria Thropheryma whippelii. Central nervous system (CNS) involvement is not rare. The most frequent CNS manifestations are cognitive and behavioural changes, sopranuclear ophtalmoplegia, myoclonus, epilepsy, ataxia, meningitis and focal cerebral palsy.