Biology subjects

Sugarman, A. L.

Publications and source records attributed to Sugarman, A. L..

5 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↗

bioRxiv2026

Long-range neural pathways for octopus chemotactile processing revealed from periphery-to-brain by centimeter-field microCT

Understanding how nervous systems mediate responses to sensation requires whole-body maps of periphery-to-brain connections. Octopuses exemplify this challenge with distributed control of eight arms and hundreds of suckers, yet their long-range microanatomical wiring remains elusive due to limitations in microscopy. We extend histotomography (Ding et al. 2019), a form of soft tissue microCT customized for volumetric characterization of cells and tissues, to centimeter range with a custom micro-CT imaging system (Ding et al., 2019). With its 10-mm field of view and 0.7-{micro}m isotropic voxels we created a high-resolution digital intact small octopus. This multi-tissue 3D blueprint enabled us to (i) elucidate previously uncharacterized chemotactile pathways from the suckers to the brain, (ii) discern subdivisions of the nerve ring connecting neighboring arms, and (iii) segment over 300 structures across organ systems at histology-like resolution. We release the labeled interactive digital specimen to facilitate collaborative whole-organism phenotyping as a practical foundation for digital organismal biology. ONE-SENTENCE SUMMARYWhole-body 3D histology reveals neural and organ architecture throughout a small octopus.

systems biology↗

bioRxiv2025

Neurons, Muscles, and Venom: Identifying Drivers of Cephalopod Predation

Venom plays a central role in the predatory ecology of coleoid cephalopods (octopuses, squids, and cuttlefish), yet the mechanisms governing venom release from the posterior salivary gland (PSG) are unknown. Using a multimodal approach combining X-ray micro-histotomography, histological stainings, in situ hybridization, comparative phylogenetics, and ex vivo imaging across multiple coleoid species, we characterize the structural and neuronal regulatory organization of the PSG. We verified that the gland comprises two distinct tubular systems: secretory tubules specialized for venom production and smooth-striated tubules positioned to facilitate venom transport toward the beak for injection into its prey. Molecular localization of filamentous and -actin confirms a circular smooth muscle layer surrounding the tubules. Mapping of six neuronal markers, including neurofilament (NF-H), synapsin, and muscle-type nicotinic acetylcholine receptors, reveals dense and stereotyped neural innervation closely associated with the muscular compartments. Comparative phylogenetic analyses of cys-loop ligand-gated ion channel sequences indicate a predominancy of excitatory acetylcholine- and dopamine-gated receptors in coleoid venom glands, implicating potential molecular agents involved in neural control of venom release. Consistent with neural regulation, ex vivo stimulation of the PSG elicits calcium signaling throughout the gland. Together, our results reveal a conserved venom gland structure among octopuses, squids, and cuttlefish, with a spatially distinct neuromuscular tissue organization indicating venom production and release sites modulated by a network of neuronal agents. This work provides a mechanistic framework into venom gland organization and molecular regulation of venom release in one of the oldest venomous lineages.

neuroscience↗

bioRxiv2023

Quantitative Geometric Modeling of Blood Cells from X-ray Histotomograms of Whole Zebrafish Larvae

Tissue phenotyping is foundational to understanding and assessing the cellular aspects of disease in organismal context and an important adjunct to molecular studies in the dissection of gene function, chemical effects, and disease. As a first step toward computational tissue phenotyping, we explore the potential of cellular phenotyping from 3-Dimensional (3D), 0.74 {micro}m isotropic voxel resolution, whole zebrafish larval images derived from X-ray histotomography, a form of micro-CT customized for histopathology. As proof of principle towards computational tissue phenotyping of cells, we created a semi-automated mechanism for the segmentation of blood cells in the vascular spaces of zebrafish larvae, followed by modeling and extraction of quantitative geometric parameters. Manually segmented cells were used to train a random forest classifier for blood cells, enabling the use of a generalized cellular segmentation algorithm for the accurate segmentation of blood cells. These models were used to create an automated data segmentation and analysis pipeline to guide the steps in a 3D workflow including blood cell region prediction, cell boundary extraction, and statistical characterization of 3D geometric and cytological features. We were able to distinguish blood cells at two stages in development (4- and 5-days-post-fertilization) and wild-type vs. polA2 huli hutu (hht) mutants. The application of geometric modeling across cell types to and across organisms and sample types may comprise a valuable foundation for computational phenotyping that is more open, informative, rapid, objective, and reproducible.

systems biology↗

bioRxiv2020

Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex

We herein report an RNA-targeting antiviral small molecule that reduces replication of the human enterovirus 71 (EV71) via stabilization of an inhibitory small molecule-RNA-protein ternary complex. The EV71 virus poses serious threats to human health, particularly in regions of Southeast Asia, and no FDA approved drugs or vaccines are available. We first screened an RNA-biased small molecule library using a peptide-displacement assay to identify ligands for the stem loop II structure of the EV71 internal ribosomal entry site, which was previously shown to impact viral translation and replication. One ligand, DMA-135, decreased viral translation and replication in cell-based studies in a dose-dependent manner with no significant toxicity. Structural, biophysical, and biochemical characterization support an allosteric mechanism in which DMA-135 induces a conformational change in the RNA structure that stabilizes a ternary complex with the AUF1 protein that then represses translation. This mechanism was further supported by pull-down experiments in cell culture. These detailed studies establish enterovirus RNA structures as promising drug targets while revealing an approach and mechanism of action that should be broadly applicable to functional RNA targeting.

biochemistry↗