Biology subjects

Warrick, J.

Publications and source records attributed to Warrick, J..

4 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↗

bioRxiv2021

Timelapse viability assay to detect division and death of primary multiple myeloma cells in response to drug treatments with single cell resolution

Heterogeneity among cancer cells and in the tumor microenvironment (TME) is thought to be a significant contributor to the heterogeneity of clinical therapy response observed between patients and can evolve over time. A primary example of this is multiple myeloma (MM), a generally incurable cancer where such heterogeneity contributes to the persistent evolution of drug resistance. However, there is a paucity of functional assays for studying this heterogeneity in patient samples or for assessing the influence of the patient TME on therapy response. Indeed, the population-averaged data provided by traditional drug response assays and the large number of cells required for screening remain significant hurdles to advancement. To address these hurdles, we developed a suite of accessible technologies for quantifying functional drug response to a panel of therapies in ex vivo three-dimensional culture using small quantities of a patients own cancer and TME components. This suite includes tools for label-free single-cell identification and quantification of both cell division and death events with a standard brightfield microscope, an open-source software package for objective image analysis and feasible data management of multi-day timelapse experiments, and a new approach to fluorescent detection of cell death that is compatible with long-term imaging of primary cells. These new tools and capabilities are used to enable sensitive, objective, functional characterization of primary MM cell therapy response in the presence of TME components, laying the foundation for future studies and efforts to enable predictive assessment drug efficacy for individual patients. Insight BoxThe new tools and capabilities described here allow new insights into functional primary cell therapy response by (i) enabling more drugs to be tested on precious and limited numbers of patient cells ex vivo (ii) providing the ability to discriminate both cell division and death events over multiple days with single-cell resolution, and (iii) by incorporating the influences of a patients own cancer cells and TME components on drug response.

bioengineering↗

bioRxiv2021

Intratumoral Heterogeneity Promotes Collective Cancer Invasion Through NOTCH1 Variation

Cellular and molecular heterogeneity within tumors has long been associated with the progression of cancer to an aggressive phenotype and a poor prognosis. However, how such intratumoral heterogeneity contributes to the invasiveness of cancer is largely unknown. Here, using a multidisciplinary approach, we investigate the interaction between molecular subtypes within bladder microtumors and the corresponding effects on their invasiveness. Our results reveal heterogeneous microtumors formed by multiple molecular subtypes possess enhanced invasiveness compared to individual cells, even when both cells are not invasive individually. To examine the molecular mechanism of intratumoral heterogeneity mediated invasiveness, live single cell biosensing, RNA interference, and CRISPR-Cas9 gene editing approaches were applied to investigate and control the composition of the microtumors. An agent-based computational model was also developed to evaluate the influence of NOTCH1 variation on DLL4 expression within a microtumor. The data indicate that variation in NOTCH1 expression can lead to upregulation of DLL4 expression within the microtumor and enhancement of microtumor invasiveness. Overall, our results reveal a novel mechanism of heterogeneity mediated invasiveness through intratumoral variation of gene expression. Summary statementThis study reveals a mechanism that Notch1 variation, instead of the average value, promotes the invasiveness of microtumor, providing a link between intratumoral heterogeneity and collective cancer invasion.

cancer biology↗

bioRxiv2020

Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer

Muscle-invasive bladder cancers have recently been characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. For example, FOXA1, GATA3, and PPARG have been shown to be essential for luminal subtype-specific regulation and subtype switching, while TP63 and STAT3 are critical for basal subtype bladder cancer. Despite these advances, the underlying epigenetic mechanism and 3D chromatin architecture for subtype-specific regulation in bladder cancers remains largely unknown. Here, we determined the genome-wide transcriptome, enhancer landscape, TF binding profiles (FOXA1 and GATA3) in luminal and basal subtypes of bladder cancers. Furthermore, we mapped genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors, for the first time in bladder cancer. We showed that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct TF binding at distal-enhancers of luminal and basal bladder cancers. Finally, we identified a novel clinically relevant transcriptional factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other luminal-specific genes (such as FOXA1, GATA3, and PPARG) and affects cancer cell proliferation and migration. In summary, our work shows a subtype-specific epigenomic and 3D genome structure in urinary bladder cancers and suggested a novel link between the circadian TF NPAS2 and a clinical bladder cancer subtype.

genomics↗