Search bioRxiv⌕ Search

Biology subjects

Bjartell, A.

Publications and source records attributed to Bjartell, A..

2 recordsLinked to original sources

Restriction-weighted q-space trajectory imaging (ResQ): Toward mapping diffusion time effects with tensor-valued diffusion encoding in human prostate cancer xenografts

PurposeTensor-valued diffusion encoding employs gradient waveforms that enable unique sensitivity to microstructural features of tissue, but the interpretation of signal and parameters may be confounded by diffusion-time dependence. We introduce a framework for restriction-weighted q-space trajectory imaging (ResQ) that incorporates diffusion-time effects via the restriction-weighting tensor, and we evaluate it in a longitudinal study of prostate cancer xenografts treated by external radiotherapy. MethodsWe proposed a novel gradient waveform design for tensor-valued encoding with controlled restriction weighting and applied a set of four waveforms at a 9.4 T preclinical MRI system. Mice were inoculated with human prostate cancer cells (LNCaP) and assigned to groups that were untreated controls or treated by external beam irradiation. ResQ produced parameters that describes the diffusion process in terms of the mean diffusivity (D), isotropic diffusional variance (VDi), and microscopic diffusion anisotropy (VDa) as well as their diffusion-time dependence ({Delta}D, {Delta}VDi, {Delta}VDa). Analyses were performed to characterize parameters longitudinally and across groups. To highlight the consequences of ignoring restriction effects, we compared ResQ to analogous parameters estimated by q-space trajectory imaging (QTI). ResultsResQ revealed clear diffusion-time dependence across all tumors, with significant longitudinal differences between treated and untreated groups, most prominent in D, {Delta}D, and VDi. The ResQ signal representation captured the signal dynamics, whereas QTI did not. Neglecting diffusion-time dependence in QTI led to substantial parameter bias, most notably a pronounced overestimation of microscopic diffusion anisotropy. ConclusionDiffusion-time effects are non-negligible in prostate cancer and must be considered when using tensor-valued diffusion encoding. The ResQ framework enables controlled restriction weighting and improved interpretability of diffusion MRI parameters compared to approaches that ignore the effects of restriction. This provides a more principled approach for tensor-valued diffusion encoding and may enable novel imaging biomarkers that disentangle diffusivity, isotropic diffusional variance, microscopic anisotropy, and their diffusion-time dependence.

biophysics↗

Quantification of microRNA editing using two-tailed RT-qPCR for improved biomarker discovery

Even though microRNAs have been viewed as promising biomarkers for years, their clinical implementation is still lagging far behind. This is in part due to the lack of RT-qPCR technologies that can differentiate between microRNA isoforms. For example, A-to-I editing of microRNAs through adenosine deaminase acting on RNA (ADAR) enzymes can affect their expression levels and functional roles, but editing isoform-specific assays are not commercially available. Here, we describe RT-qPCR assays that are specific for editing isoforms, using microRNA-379 (miR-379) as a model. The assays are based on two-tailed RT-qPCR, and we show them to be compatible both with SYBR Green and hydrolysis-based chemistries, as well as with both qPCR and digital PCR. The assays could readily detect different miR-379 editing isoforms in various human tissues. We found that the miR-379 editing frequency was higher in prostate cancer samples compared to benign prostatic hyperplasia samples. Furthermore, decreased expression of unedited miR-379, but not edited miR-379, was associated with treatment resistance, metastasis and shorter overall survival. Taken together, this study presents the first RT-qPCR assays that were demonstrated to distinguish A-to-I-edited microRNAs, and shows that they can be useful in the identification of biomarkers that previously have been masked by other isoforms. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/448409v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@79afcorg.highwire.dtl.DTLVardef@15028deorg.highwire.dtl.DTLVardef@1ab3fe9org.highwire.dtl.DTLVardef@1f11760_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗