Researchers led by Kay Huebner at Ohio State University report in Modern Pathology on their assessment of stem cell subpopulations found in metastatic and primary breast cancer tumors. They examined the expression of CD44, CD24, vimentin, and E-cadherin — to evaluate stem-like and mesenchymal cell properties — in two breast cancer patient cohorts. From this, they found that the occurrence of CD24−/44+ and CD24+/44− cells did not differ between primary and metastatic lesions, while E-cadherin and vimentin expression did. This, the researchers say, indicates that "the frequency of CD24−/44+ cells does not differ in metastases relative to the primary breast cancer but differs by tumor stage and subtype."

Also in Modern Pathology, Stanford University's Robert West and colleagues present their study of the phosphatidylinositol-3-kinase pathway in breast columnar cell lesions. They looked at PIK3CA and AKT1 mutations, among other "known activating point mutations," in 23 samples of columnar cell lesions and matched normal breast tissue or concurrent carcinoma samples. They found that "columnar cell lesions and carcinoma were frequently discordant for PIK3CA/AKT1 mutation status," with PIK3CA mutations being common in columnar cell lesions. "Although these findings need validation in a larger study, they raise a number of interesting questions as to the biologic/precursor potential of breast columnar cell lesions, and the role ofPIK3CA/AKT1 mutations in breast carcinogenesis," the researchers write.

Baylor College of Medicine investigators present a one-step mitochondrial genome analysis approach in Clinical Chemistry. By combining long-range PCR and massively parallel sequencing, the Baylor researchers were able to detect point mutations as well as large deletions in mtDNA. They analyzed 45 samples and determined that their approach had 100 percent diagnostic sensitivity and specificity as compared to Sanger sequencing results. "This one-step comprehensive approach makes qualitative and quantitative calls for every nucleotide position of the entire mitochondrial genome. It can simultaneously detect large mtDNA deletions as well as small indels, identifying both the breakpoints and the degree of heteroplasmy," the researchers write. "We believe this novel approach will greatly facilitate the diagnosis of mitochondrial diseases in a timely and cost-effective fashion."

In a review in Clinical Chemistry, researchers at the University of Oxford say that meta-analyses of biomarker studies "have the power to provide robust evidence to support our understanding of the role of novel biomarkers for disease," though they also have a number of limitations. The authors draw on two examples of biomarkers for cardiovascular disease risk — homocysteine and triglycerides — and how meta-analyses of those have helped generate hypotheses but also misleading findings. However, they note that additional information from randomized controlled trials and genetic studies may help refine the roles of biomarkers in predicting cardiovascular disease.

In the Journal of Molecular Diagnostics, researchers from the University of Florence in Italy present a high-resolution melting protocol to screen for mutations in thyroid nodules. They use their high-resolution melting approach to screen for mutations in the KRAS, HRAS, NRAS, and BRAF oncogenes in thyroid fine-needle aspiration biopsies, and using this approach, they found that 15 percent of their samples contained oncogene variants — similar to other reports — and they identified two samples with rare KRAS mutation that had not been linked to thyroid cancer before. "In addition to establishing the evident advantages of HRM prescreening in terms of time and economic improvement, this pilot study confirmed the accuracy of the proposed method. Complete concordance was found between the standard protocol, based on sequencing of all samples, and the HRM-based screening," the authors write.

Also in the Journal of Molecular Diagnostics, researchers led by the University of Houston's Richard Willson report on using a broadly sensitive RT-PCR approach coupled with mass spectrometry to identify dengue virus strains. Specifically, their protocol combines PCR with matrix-assisted laser desorption/ionization-time of flight analysis of digested PCR fragments. Those results are then compared to a mass database of 2,517 strains of dengue. "The methodology was successfully demonstrated experimentally by identifying the serotypes of eight test strains using mosquito cell cultures infected with strains of all four serotypes and with full-length cDNA clones," Willson and his colleagues report.

In an online, advance Experimental and Molecular Pathology article, Ronald van Eijk and his colleagues at Leiden University Medical Center report their assessment of an automated DNA/RNA isolation system for FFPE samples. The system "can process 48 tissue samples in three [hours] and 15 [minutes] using silica-coated magnetic nanoparticles. The process integrates both lysis and deparaffinization by hydrophobic adsorption instead of offline xylene-based deparaffinization," van Eijk et al. write. They compared the quality of how the automated system could isolate and detect KRAS and BRAF mutations from tissue cores and microdissections to the current, manual approach. "The first results of using DNA obtained from the fully automated system in Sanger sequencing demonstrate that the overall quality of the sequences is higher than in the classical process," the researchers write. They note that Siemens Healthcare Diagnostics provided them with the kits needed to evaluate the system, and supported the manuscript preparation.

Also in Experimental and Molecular Pathology, researchers led by James Graham Brown Cancer Center's Joongho Joh say they have developed assays to detect and diagnose MusPV, a mouse papilloma virus, in laboratory mice. They designed primers specific for MusPV to detect the virus in mouse tumors using PCR. "The selected primer set, designated as MusPV-My09/11, amplified specifically MusPV without producing any non-specific bands," the researchers write. "This set of primers failed to bind to MnPV or MmiPV genomic DNAs, differentiating MusPV from other known rodent PVs, or DNAs from uninfected tail tissues." The researchers add that "it is important to develop and evaluate diagnostic methods to screen mouse colonies for the presence of MusPV because it is an emerging new mouse pathogen that might have deleterious effects on breeding as well as studies involving immunodeficient mice."

Researchers led by Miraca Life Sciences' Richard Lash report in the Journal of Clinical Pathology that material from biopsies can be used to determine KRAS mutational status in colorectal cancer patients. Using both PCR and Sanger sequencing, the researchers performed KRAS mutational analysis on biopsy and surgical resection specimens from 30 colorectal cancer patients. They found that 40 percent of the tumors had KRAS mutations and that there was 100 percent correlation between biopsy and resection specimens. Lash and his colleagues write that this study supports "the reliability of using endoscopic biopsy specimens for the assessment of KRAS status before anti-EGFR therapy."

Also in the Journal of Clinical Pathology, Brazilian researchers present their work evaluating whether NF-κB expression can be used to predict radiotherapy response in advanced cervical cancer patients. The researchers examined NF-κB-p65 and NF-κB-p50 expression in 32 patients with stage IB2 and IIB cervical cancer before they underwent radiotherapy. Expression levels were also determined 12 patients who had residual tumors after radiotherapy. While the researchers found that most patients expressed NF-κB in the cytoplasm prior to radiotherapy, such expression could not be used to predict which patients would have residual disease.

US President Barack Obama has signed the Food and Drug Administration Safety and Innovation Act, reports The Hill's Healthwatch Blog. The bill, which was passed in its final form by Congress last month, re-authorizes FDA to collect user fees from drug and medical device companies to fund the agency's review process. As our sister publication GenomeWeb Daily News has noted, under this bill FDA will be able to collect an additional $308 million over the course of five years, which will allow the agency to streamline its regulatory processes — hiring 200 new employees — as well as improve the agency's "transparency, efficiency, and consistency."

The Hill's Healthwatch Blog notes that Health and Human Services Secretary Kathleen Sebelius praised the legislation Monday. "S. 3187 is the culmination of the work of the administration and Congress, in partnership with patients, the pharmaceutical and medical device industries, the clinical community, and other stakeholders, to provide the Food and Drug Administration with the tools needed to continue to bring drugs and devices to market safely and quickly and promote innovation in the biomedical industry, and to help secure the jobs supported by drug and device development," she said in a statement.