Biology subjects

Shapiro, E. M.

Publications and source records attributed to Shapiro, E. M..

6 recordsLinked to original sources

bioRxiv2024

Predicting Inhibitors of OATP1B1 via Heterogeneous OATP-Ligand Interaction Graph Neural Network (HOLI-GNN)

Organic anion transporting polypeptides (OATPs) are membrane transporters crucial for drug uptake and distribution in the human body. OATPs can mediate drug-drug interactions (DDIs) in which the interaction of one drug with an OATP impairs the uptake of another drug, resulting in potentially fatal pharmacological effects. Predicting OATP-mediated DDIs is challenging, due to limited information on OATP inhibition mechanisms and inconsistent experimental OATP inhibition data across different studies. This study introduces Heterogeneous OATP-Ligand Interaction Graph Neural Network (HOLIgraph), a novel computational model that integrates molecular modeling with a graph neural network to enhance the prediction of drug-induced OATP inhibition. By combining ligand (i.e., drug) molecular features with protein-ligand interaction data from rigorous docking simulations, HOLIgraph outperforms traditional DDI prediction models which rely solely on ligand molecular features. HOLIgraph achieved a median balanced accuracy of over 90 percent when predicting inhibitors for OATP1B1, significantly outperforming purely ligand-based models. Beyond improving inhibition prediction, the data used to train HOLIgraph can enable the characterization of protein residues involved in inhibitory drug-OATP interactions. We identified certain OATP1B1 residues that preferentially interact with inhibitors, including I46 and K49. We anticipate such interaction information will be valuable to future structural and mechanistic investigations of OATP1B1. Scientific ContributionHOLIgraph introduces a new paradigm for DDI prediction by incorporating protein-ligand interactions derived from docking simulations into a graph neural net framework. This approach, enabled by recent structural breakthroughs for OATP1B1, represents a significant departure from traditional models that rely only on ligand features. By achieving high predictive accuracy and uncovering mechanistic insights, HOLIgraph sets a new trajectory for computational tools in drug design and DDI prediction.

bioengineering↗

bioRxiv2023

MRI of OATP-expressing transplanted cells using clinical doses of gadolinium contrast agent

Hepatic organic anion transporting polypeptides (OATPs) transport off-the-shelf, FDA-approved, hepatospecific Gd-based MRI contrast agents into cells that express the transporters enhancing signal on clinical T1-weighted MRI. Studies have used MRI to identify OATP-overexpressing tumors and metastases in mice following the delivery of Gd-EOB-DTPA at 27-67-fold higher than clinical doses. With safety and regulatory concern over Gd-based contrast agents, translation of this imaging paradigm to humans for regenerative medicine cell therapy will require substantially lower doses of agent. Here we complemented static T1-weighted MRI and/or T1-mapping with dynamic contrast enhanced (DCE)-MRI and show that even low intracellular accumulation of contrast agent results in a sustained signal enhancement in OATP-overexpressing tumors while control, non-expressing tumors have rapid wash-in and wash-out dynamics which could be distinguished by performing area-under-the-curve (AUC) analyses.

bioengineering↗

bioRxiv2023

MRI-based cell tracking of OATP-expressing cell transplants by pre-labeling with Gd-EOB-DTPA

PurposeTo detect cell transplants labeled with a clinical gadolinium-based contrast agent as hyperintense signals using a clinically familiar T1-weighted MRI protocol. MethodsHEK293 cells were stably transduced to express human OATP1B3, a hepatic transporter that transport Gd-EOB-DTPA into cells that express the transporters, the intracellular accumulation of which cells causes signal enhancement on T1-weighted MRI. Cells were labeled in media containing Gd-EOB-DTPA for MRI evaluation and indocyanine green for cryofluorescence tomography validation. Labeled cells were injected into chicken hearts, in vitro, after which MRI and cryofluorescence tomography were performed in tandem. ResultsOATP1B3-expressing cells had substantially reduced T1 following labeling with Gd-EOB-DTPA in culture. Following their implantation into chicken heart, these cells were easily identified in T1-weighted MRI. Cryofluorescence tomography validated that the areas of signal enhancement in MRI overlapped with areas of indocyanine green signal, indicating that signal enhancement was due to the transplanted cells. ConclusionOATP1B3-expressing cells can be pre-labeled with Gd-EOB-DTPA prior to injection into tissue, affording the use of clinically familiar T1-weighted MRI to robustly detect cell transplants.

bioengineering↗

bioRxiv2023

Radiopaque Implantable Biomaterials for Nerve Repair

Repairing peripheral nerve injuries remains a clinical challenge. To enhance nerve regeneration and functional recovery, the use of auxiliary implantable biomaterial conduits has become widespread. After implantation, there is currently no way to assess the location or function of polymeric biomedical devices, as they cannot be easily differentiated from surrounding tissue using clinical imaging modalities. Adding nanoparticle contrast agents into polymer matrices can introduce radiopacity and enable imaging using computed tomography (CT), but radiopacity must be balanced with changes in material properties that impact device function and biological response. In this study radiopacity was introduced to porous films of polycaprolactone (PCL) and poly(lactide-co-glycolide) (PLGA) 50:50 and 85:15 with 0-40wt% biocompatible tantalum oxide (TaOx) nanoparticles. To achieve radiopacity, at least 5wt% TaOx was required, with [≥] 20wt% TaOx leading to reduced mechanical properties and increased nano-scale surface roughness of films. As polymers used for peripheral nerve injury devices, films facilitated nerve regeneration in an in vitro co-culture model of glia (Schwann cells) and dorsal root ganglion neurons (DRG), measured by expression markers for myelination. The ability of radiopaque films to support nerve regeneration was determined by the properties of the polymer matrix, with a range of 5-20wt% TaOx balancing both imaging functionality with biological response and proving that in situ monitoring of nerve repair devices is feasible.

bioengineering↗

bioRxiv2020

Dynamic contrast enhanced MRI with clinical hepatospecific MRI contrast agents in pigs: initial experience

Pigs are an important translational research model for biomedical imaging studies, and especially for modeling diseases of the liver. Dynamic contrast enhanced (DCE)-MRI is experimentally used to measure liver function in humans, but has never been characterized in pig liver. Here we performed DCE-MRI of pig liver following the delivery of two FDA approved hepato-specific MRI contrast agents, Gd-EOB-DTPA (Eovist) and Gd-BOPTA (Multihance), and the non-hepatospecific agent Magnevist, and optimized the anesthesia and animal handling protocol to acquire robust data. A single pig underwent 5 scanning sessions over six weeks, each time injected at clinical dosing either with Eovist (twice), Multihance (twice) or Magnevist (once). DCE-MRI was performed at 1.5T for 60 minutes. DCE-MRI showed rapid hepatic MRI signal enhancement following IV injection of Eovist or Multihance. Efflux of contrast agent from liver exhibited kinetics similar to that in humans, except for one hyperthermic animal where efflux was very fast. As expected, Magnevist was non-enhancing in the liver. The hepatic signal enhancement from Eovist matched that seen in humans and primates, while the hepatic signal enhancement from Multihance was different, similar to rodents and dogs, likely the result of differential hepatic organic anion transport polypeptides. This first experience with these agents in pigs provides valuable information on contrast agent dynamics in normal pig liver. Given the disparity in contrast agent uptake kinetics with humans for Multihance, Eovist should be used in porcine models for biomedical imaging. Proper animal health maintenance, especially temperature, seems essential for accurate and reproducible results.

physiology↗

bioRxiv2018

Age-dependent visualization of neural progenitor cells within the rostral migratory stream via MRI and endogenously labeled micron-sized iron oxide particles

The subventricular zone (SVZ) is one of the primary sources for rodent neural progenitor cells (NPC), however, aging greatly impacts the substructure of the region and rate of new cell birth. To determine if age impacts the rate of in vivo migration within animals, we examined the rostral migratory stream (RMS) of animals across 12 days using an established MRI technique. To visualize NPCs, we injected micron sized particles of iron oxide (MPIO) into the lateral ventricle to endogenously label cells within the SVZ, which then appeared as hypo-intensive spots within MR images. Our in vivo MRI data showed that the rate of migration was significantly different between all ages examined, with decreases in the distance traveled as age progressed. The total number of iron oxide labeled cells within the olfactory bulb on day 12, decrease significantly when compared across ages in ex vivo high-resolution scans. We also, for the first time, demonstrated the endogenous labeling of cells within the dentate gyrus (DG) of hippocampus. Here too, there was a significant decrease in the number of labeled cells within the structure across age. Histology of the NPCs verified the decrease in labeling of cells with doublecortin (DCX) as age progressed for both regions. The dramatic reduction of labeling in NPCs within the SVZ and DG observed with MRI, demonstrates the importance of understanding the impact of age on the relationship of NPC and disease.

neuroscience↗