Biology subjects

Parkinson, D.

Publications and source records attributed to Parkinson, D..

3 recordsLinked to original sources

bioRxiv2026

Label-free 3D virtual histology of human formalin-fixed paraffin-embedded (FFPE) prostate needle biopsies with propagation-based phase-contrast micro-CT (PBCT)

For over a century, the goal of estimating clinical outcome from tumor biopsies has been based on histomorphology of 2D tissue slices that represent a small fraction of collected samples. Its power derives from histologys 1) unbiased representation of cell types, 2) subcellular resolution that allows the characterization of health and disease states across cell types, and 3) multi-millimeter fields of view that allow assessment of tumor heterogeneity. Histologys dependence upon physical slices, however, limits assessment of 3-dimensional cellular volumes and tissue architecture. Here, we used propagation-based phase-contrast micro-CT (PBCT) to create 3D histological images of residual formalin-fixed, paraffin-embedded (FFPE) prostate needle biopsies. The resulting isotropic, grey-scale, 0.5 micron voxel matrices were used to explore the potential of for the 3D virtual histology to distinguish diagnostic categories including benign prostatic tissue and prostatic adenocarcinoma of Gleason patterns 3, 4, and 5. Maximum intensity projections of stacks of digital slices totaling 5 microns "slices" allowed the study of virtual sections corresponding to actual serial H&E-stained sections of tissue cut after micro-CT imaging. Like histology, our PBCT reconstructions allowed us to distinguish between non-infiltrative and undulating glands of benign prostatic tissue, infiltrative round glands of Gleason pattern 3, cribriform structures of Gleason pattern 4, and comedonecrosis of Gleason pattern 5. Unlike histology, micro-CT allowed us to further probe 3D tissue architecture in volumetric context. User-friendly exploration of sample volumes was achieved using a customized Neuroglancer multiplanar and 3D rendering interface. Sparsely trained cycleGAN produced plausible virtual H&E staining from the unstained micro-CT reconstructions. Unlike tissue-section based histology, micro-CT-based virtual histology yields nondestructive 3D characterization of cancer cell and tissue architecture, including glandular spaces, without the undersampling or cutting artifacts of histology. These findings demonstrate the feasibility of PBCT-based 3D virtual histology of prostate cancer and suggest the exploration of derived quantitative analyses of tumor properties for potential contributions to patient care.

pathology↗

bioRxiv2025

Variable Schwann cell merlin inactivation is targetable with TEAD1 inhibition in schwannomas.

Schwann cell tumors occur frequently in association with the vestibular nerves, leading to sensorineural hearing loss, and brainstem compression. In humans, unilateral vestibular schwannomas (VS) occur sporadically (VSspo)1, or bilaterally with neurofibromatosis type 2 syndrome (NF2) - VSnf2.2 VS formation is driven by sub-haploid NF2 gene dosage3, typically by biallelic loss.4,5 Loss of merlin promotes hippo/TEAD dependent transcriptional reprogramming, proliferation, and paracrine signaling that varies across time, and tumor volume.4,6 These variations lead to a clinically unpredictable course, and incomplete response to treatment. We hypothesized that Schwann cell merlin inactivation state determines cell-wise hippo/TEAD dependency and drives schwannoma pathogenesis. We analyzed clinical samples from VSspo and VSnf2 with a multi-omics approach and detected variation in merlin activity within tumor Schwann cell population. We found that tumor-driving merlin-depleted Schwann cells (Schwannmer-) exhibited elevated hippo activity that was predominantly driven by TEAD1. In-silico TEAD1 perturbation led to a reversal to merlin intact Schwann phenotype. These findings, and tumor cell growth suppression were confirmed in NF2fl/fl;Peri-Cre mouse model7, and in human derived schwannoma cells treated with a pan-TEAD auto palmitoylation inhibitor VT3989.8 Our computational and experimental results confirm that TEAD1 inhibition could be a potent, targeted strategy for schwannomas.

cancer biology↗

bioRxiv2021

A Wide-Field Micro-Computed Tomography Detector: Micron Resolution at Half-centimeter Scale

Ideal 3-dimensional imaging of many complex samples, such as biological tissues made up of micro-scale structures extending over millimeter- to centimeter-scale tissue samples and organisms, requires both a wide field-of-view and high resolution. With existing optics and detectors used for micro-CT imaging, sub-micron pixel resolution can only be achieved for fields-of-view of <2 mm. This manuscript presents a unique detector system with a 6-mm field-of-view image circle and 0.5 m pixel size that can be used in both synchrotron facilities and tabletop micro-CT units. A resolution-test pattern with linear microstructures and whole adult Daphnia magna were imaged on Beamline 8.3.2 of the Advanced Light Source. Volumes of 10,000 x 10,000 x 7,096 isotropic 0.5 m voxels were reconstructed over a 5.0 x 3.5 mm field-of-view. Measurements in the projection domain confirmed a 1.182 m measured spatial resolution that is largely Nyquist-limited. This unprecedented combination of field-of-view and resolution dramatically reduces the need for sectional scans and computational stitching for large samples, ultimately offering the means to elucidate change in tissue and cellular morphology in the context of larger whole, intact model organisms and specimens. This development is also anticipated to benefit micro-CT imaging in materials science, microelectronics, agricultural science, and biomedical engineering. SynopsisA custom wide-field lens and a new-generation megapixel camera enabled microCT scanning over a 3.5 x 5 mm field-of-view at a 1 m resolution / 0.5 m pixel size at the Berkeley Lawrence Advanced Light Source using a phantom with micron scale features. This novel combination of resolution and field-of-view will be broadly applicable to any setting in which micron-scale structures need to be characterized comprehensively in 3 dimensions over mm to cm scale.

bioinformatics↗