Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens

Background: Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffinembedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. The former limits accurate correlation whilst the latter is impractical when utilizing rare or limited archived specimens. Principal Findings: For effective recovery of genomic DNA and total RNA from a single FFPE specimen, without splitting the proteinase-K digested tissue solution, we optimized a co-extraction method by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll TM Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and-RNA. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells. These experiments show that the TRIzol-based co-extraction method provides larger amounts of FFPE-DNA and –RNA tha

Expression analysis of genes associated with human osteosarcoma tumors shows correlation of RUNX2 overexpression with poor response to chemotherapy

Background: Human osteosarcoma is the most common pediatric bone tumor. There is limited understanding of the molecular mechanisms underlying osteosarcoma oncogenesis, and a lack of good diagnostic as well as prognostic clinical markers for this disease. Recent discoveries have highlighted a potential role of a number of genes including: RECQL4, DOCK5, SPP1, RUNX2, RB1, CDKN1A, P53, IBSP, LSAMP, MYC, TNFRSF1B, BMP2, HISTH2BE, FOS, CCNB1, and CDC5L. Methods: Our objective was to assess relative expression levels of these 16 genes as potential biomarkers of osteosarcoma oncogenesis and chemotherapy response in human tumors. We performed quantitative expression analysis in a panel of 22 human osteosarcoma tumors with differential response to chemotherapy, and 5 normal human osteoblasts.Results: RECQL4, SPP1, RUNX2, and IBSP were significantly overexpressed, and DOCK5, CDKN1A, RB1, P53, and LSAMP showed significant loss of expression relative to normal osteoblasts. In addition to being overexpressed in osteosarcoma tumor samples relative to normal osteoblasts, RUNX2 was the only gene of the 16 to show significant overexpression in tumors that had a poor response to chemotherapy relative to good responders. Conclusion: These data underscore the loss of tumor suppressive pathways and activation of specific oncogenic mechanisms associated with osteosarcoma oncogenesis, while drawing attention to the role of RUNX2 expression as a potential biomarker of chemotherapy failure in osteosarcoma. © 2010 Sadikovic et al; licensee BioMed Central Ltd

The effects of an evidence- and theory-informed feedback intervention on opioid prescribing for non-cancer pain in primary care: a controlled interrupted time series analysis.

BACKGROUND: The rise in opioid prescribing in primary care represents a significant international public health challenge, associated with increased psychosocial problems, hospitalisations, and mortality. We evaluated the effects of a comparative feedback intervention with persuasive messaging and action planning on opioid prescribing in primary care. METHODS AND FINDINGS: A quasi-experimental controlled interrupted time series analysis used anonymised, aggregated practice data from electronic health records and prescribing data from publicly available sources. The study included 316 intervention and 130 control primary care practices in the Yorkshire and Humber region, UK, serving 2.2 million and 1 million residents, respectively. We observed the number of adult patients prescribed opioid medication by practice between July 2013 and December 2017. We excluded adults with coded cancer or drug dependency. The intervention, the Campaign to Reduce Opioid Prescribing (CROP), entailed bimonthly, comparative, and practice-individualised feedback reports to practices, with persuasive messaging and suggested actions over 1 year. Outcomes comprised the number of adults per 1,000 adults per month prescribed any opioid (main outcome), prescribed strong opioids, prescribed opioids in high-risk groups, prescribed other analgesics, and referred to musculoskeletal services. The number of adults prescribed any opioid rose pre-intervention in both intervention and control practices, by 0.18 per 1,000 adults per month, respectively. During the intervention period, prescribing per 1,000 adults fell in intervention practices and continued rising in control practices, with a difference of -0.65 per 1,000 patients, corresponding to 15,000 fewer patients prescribed opioids. These trends continued post-intervention, although at slower rates. Prescribing of strong opioids, total opioid prescriptions, and prescribing in high-risk patient groups also generally fell. Prescribing of other analgesics fell whilst musculoskeletal referrals did not rise. Effects were attenuated after feedback ceased. Study limitations include being limited to 1 region in the UK, possible coding errors in routine data, being unable to fully account for concurrent interventions, and uncertainties over how general practices actually used the feedback reports and whether reductions in prescribing were always clinically appropriate. CONCLUSIONS: Repeated comparative feedback offers a promising and relatively efficient population-level approach to reduce opioid prescribing in primary care, including prescribing of strong opioids and prescribing in high-risk patient groups. Such feedback may also prompt clinicians to reconsider prescribing other medicines associated with chronic pain, without causing a rise in referrals to musculoskeletal clinics. Feedback may need to be sustained for maximum effect