Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets.

BACKGROUND: Batch effects are a persistent and pervasive form of measurement noise which undermine the scientific utility of high-throughput genomic datasets. At their most benign, they reduce the power of statistical tests resulting in actual effects going unidentified. At their worst, they constitute confounds and render datasets useless. Attempting to remove batch effects will result in some of the biologically meaningful component of the measurement (i.e. signal) being lost. We present and benchmark a novel technique, called Harman. Harman maximises the removal of batch noise with the constraint that the risk of also losing biologically meaningful component of the measurement is kept to a fraction which is set by the user. RESULTS: Analyses of three independent publically available datasets reveal that Harman removes more batch noise and preserves more signal at the same time, than the current leading technique. Results also show that Harman is able to identify and remove batch effects no matter what their relative size compared to other sources of variation in the dataset. Of particular advantage for meta-analyses and data integration is Harman's superior consistency in achieving comparable noise suppression - signal preservation trade-offs across multiple datasets, with differing number of treatments, replicates and processing batches. CONCLUSION: Harman's ability to better remove batch noise, and better preserve biologically meaningful signal simultaneously within a single study, and maintain the user-set trade-off between batch noise rejection and signal preservation across different studies makes it an effective alternative method to deal with batch effects in high-throughput genomic datasets. Harman is flexible in terms of the data types it can process. It is available publically as an R package ( https://bioconductor.org/packages/release/bioc/html/Harman.html ), as well as a compiled Matlab package ( http://www.bioinformatics.csiro.au/harman/ ) which does not require a Matlab license to run.

Long-term exposure to commercially available sunscreens containing nanoparticles of TiO2 and ZnO revealed no biological impact in a hairless mouse model.

BACKGROUND: The application of sunscreen is a critical component of a sun-safe strategy, however the possibility of unexpected, adverse outcomes resulting from long-term use of sunscreens containing nanoparticles of titanium dioxide (TiO2) and zinc oxide (ZnO) has not yet been examined. Here, immune-competent hairless mice were exposed over a 36-week period to weekly topical applications of sunscreens containing nanoparticles of ZnO or TiO2, or no metal oxide nanoparticles, with or without subsequent exposure to ultraviolet radiation (UVR). Control groups received no sunscreen applications, with or without UVR. RESULTS: Mice exposed to UVR in the absence of sunscreen developed statistically significant incidences of histologically-diagnosed malignant and benign skin neoplasms, whereas no statistically significant adverse biological outcomes were found in mice treated with the sunscreens containing ZnO or TiO2 nanoparticles. Elevated levels of Ti were detected in the livers of mice treated with sunscreen containing TiO2 nanoparticles compared to untreated control, but total Zn concentrations did not significantly alter in any major organs except for the skin of mice treated with ZnO sunscreen. Exposure to UVR did not have a significant impact on examined tissue concentrations of Zn or Ti. Few to no transcriptional changes were found in ZnO or TiO2-treated groups, but mice treated with the sunscreen containing only organic filters showed substantial gene disregulation. CONCLUSIONS: Taken together with previous work, this long-term study provided no basis to avoid the use of sunscreens containing metal oxide nanoparticles.

LipiD-QuanT: a novel method to quantify lipid accumulation in live cells.

Lipid droplets (LDs) are the main storage organelles for triglycerides. Elucidation of lipid accumulation mechanisms and metabolism are essential to understand obesity and associated diseases. Adipogenesis has been well studied in murine 3T3-L1 and human Simpson-Golabi-Behmel syndrome (SGBS) preadipocyte cell lines. However, most techniques for measuring LD accumulation are either not quantitative or can be destructive to samples. Here, we describe a novel, label-free LD quantification technique (LipiD-QuanT) to monitor lipid dynamics based on automated image analysis of phase contrast microscopy images acquired during in vitro human adipogenesis. We have applied LipiD-QuanT to measure LD accumulation during differentiation of SGBS cells. We demonstrate that LipiD-QuanT is a robust, nondestructive, time- and cost-effective method compared with other triglyceride accumulation assays based on enzymatic digest or lipophilic staining. Further, we applied LipiD-QuanT to measure the effect of four potential pro- or antiobesogenic substances: DHA, rosiglitazone, elevated levels of D-glucose, and zinc oxide nanoparticles. Our results revealed that 2 µmol/l rosiglitazone treatment during adipogenesis reduced lipid production and caused a negative shift in LD diameter size distribution, but the other treatments showed no effect under the conditions used here.

Dermal absorption and short-term biological impact in hairless mice from sunscreens containing zinc oxide nano- or larger particles.

Previous studies have shown no, or very limited, skin penetration of metal oxide nanoparticles following topical application of sunscreens, yet concerns remain about their safety compared to larger particles. Here, we assessed the comparative dermal absorption of a traceable form of Zn ((68)Zn) from (68)ZnO nano-sized and larger particles in sunscreens. Sunscreens were applied to the backs of virgin or pregnant hairless mice over four days. Control groups received topical applications of the sunscreen formulation containing no ZnO particles, or no treatment. Major organs were assessed for changes in (68)Zn/(64)Zn ratios, (68)Zn tracer and total Zn concentrations. Short-term biological impact was assessed by measuring levels of serum amyloid A in blood, and by performing whole-genome transcriptional profiling on livers from each group. Increased concentrations of (68)Zn tracer were detected in internal organs of mice receiving topical applications of (68)ZnO (nano-sized and larger particles), as well as in fetal livers from treated dams, compared with controls. Furthermore, concentrations of (68)Zn in organs of virgin mice treated with sunscreen containing (68)ZnO nanoparticles were found to be significantly higher than in mice treated with sunscreen containing larger (68)ZnO particles. However, no ZnO-mediated change in total Zn concentration in any of the major organs was observed. Thus, despite (68)Zn absorption, which may have been in the form of soluble (68)Zn species or (68)ZnO particles (not known), Zn homeostasis was largely maintained, and the presence of ZnO particles in sunscreen did not elicit an adverse biological response in the mice following short-term topical applications.

Surface coatings of ZnO nanoparticles mitigate differentially a host of transcriptional, protein and signalling responses in primary human olfactory cells.

BACKGROUND: Inhaled nanoparticles have been reported in some instances to translocate from the nostril to the olfactory bulb in exposed rats. In close proximity to the olfactory bulb is the olfactory mucosa, within which resides a niche of multipotent cells. Cells isolated from this area may provide a relevant in vitro system to investigate potential effects of workplace exposure to inhaled zinc oxide nanoparticles. METHODS: Four types of commercially-available zinc oxide (ZnO) nanoparticles, two coated and two uncoated, were examined for their effects on primary human cells cultured from the olfactory mucosa. Human olfactory neurosphere-derived (hONS) cells from healthy adult donors were analyzed for modulation of cytokine levels, activation of intracellular signalling pathways, changes in gene-expression patterns across the whole genome, and compromised cellular function over a 24 h period following exposure to the nanoparticles suspended in cell culture medium. RESULTS: ZnO nanoparticle toxicity in hONS cells was mediated through a battery of mechanisms largely related to cell stress, inflammatory response and apoptosis, but not activation of mechanisms that repair damaged DNA. Surface coatings on the ZnO nanoparticles mitigated these cellular responses to varying degrees. CONCLUSIONS: The results indicate that care should be taken in the workplace to minimize generation of, and exposure to, aerosols of uncoated ZnO nanoparticles, given the adverse responses reported here using multipotent cells derived from the olfactory mucosa.

Durability and inflammogenic impact of carbon nanotubes compared with asbestos fibres.

BACKGROUND: It has been suggested that carbon nanotubes might conform to the fibre pathogenicity paradigm that explains the toxicities of asbestos and other fibres on a continuum based on length, aspect ratio and biopersistence. Some types of carbon nanotubes satisfy the first two aspects of the fibre paradigm but only recently has their biopersistence begun to be investigated. Biopersistence is complex and requires in vivo testing and analysis. However durability, the chemical mimicking of the process of fibre dissolution using in vitro treatment, is closely related to biopersistence and more readily determined. Here, we describe an experimental process to determine the durability of four types of carbon nanotubes in simulated biological fluid (Gambles solution), and their subsequent pathogenicity in vivo using a mouse model sensitive to inflammogenic effects of fibres. The in vitro and in vivo results were compared with well-characterised glass wool and asbestos fibre controls. RESULTS: After incubation for up to 24 weeks in Gambles solution, our control fibres were recovered at percentages consistent with their known in vitro durabilities and/or in vivo persistence, and three out of the four types of carbon nanotubes tested (single-walled (CNTSW) and multi-walled (CNTTANG2, CNTSPIN)) showed no, or minimal, loss of mass or change in fibre length or morphology when examined by electron microscopy. However, the fourth type [multi-walled (CNTLONG1)] lost 30% of its original mass within the first three weeks of incubation, after which there was no further loss. Electron microscopy of CNTLONG1 samples incubated for 10 weeks confirmed that the proportion of long fibres had decreased compared to samples briefly exposed to the Gambles solution. This loss of mass and fibre shortening was accompanied by a loss of pathogenicity when injected into the peritoneal cavities of C57Bl/6 mice compared to fibres incubated briefly. CNTSW did not elicit an inflammogenic effect in the peritoneal cavity assay used here. CONCLUSIONS: These results support the view that carbon nanotubes are generally durable but may be subject to bio-modification in a sample-specific manner. They also suggest that pristine carbon nanotubes, either individually or in rope-like aggregates of sufficient length and aspect ratio, can induce asbestos-like responses in mice, but that the effect may be mitigated for certain types that are less durable in biological systems. Results indicate that durable carbon nanotubes that are either short or form tightly bundled aggregates with no isolated long fibres are less inflammogenic in fibre-specific assays.