Dataset Information

Tissue-specific Fixation Methods Are Required for Optimal In Situ Visualization of Hyaluronan in the Ovary, Kidney, and Liver.

ABSTRACT: Hyaluronan (HA) is a ubiquitous component of the extracellular matrix. The spatial-temporal localization of HA can be visualized in situ using biotinylated HA binding proteins (HABPs). This assay is sensitive to fixation conditions, and there are currently no best practices for HA detection. Thus, the goal of this study was to optimize fixation conditions for visualizing HA in the ovary, kidney, and liver through analysis of six commonly used fixatives for HA detection: Bouin's Solution, Carnoy's Solution, Ethanol-Formalin-Glacial Acetic Acid (EFG), Histochoice, Modified Davidson's Solution, and 10% Neutral Buffered Formalin. Organs were harvested from CB6F1 mice and fixed with one of the identified fixatives. Fixed organs were sectioned, and the HABP assay was performed on sections in parallel. Hematoxylin and eosin staining was also performed to visualize tissue architecture. HABP signal localization and intensity varied between fixatives. EFG and Carnoy's Solution best preserved the HA signal intensity in the ovary and liver, showing HA localization in various sub-organ structures. In the kidney, only Modified Davidson's Solution was less than optimal. Our findings demonstrate that fixation can alter the ability to detect HA in tissue macro- and microstructures, as well as localization in a tissue-specific manner, in situ.

SUBMITTER: Rowley JE

PROVIDER: S-EPMC6931168 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Tissue-specific Fixation Methods Are Required for Optimal In Situ Visualization of Hyaluronan in the Ovary, Kidney, and Liver.

Rowley Jennifer E JE Rubenstein Gillian E GE Manuel Sharrόn L SL Johnson Natalie L NL Surgnier Jordan J Kapitsinou Pinelopi P PP Duncan Francesca E FE Pritchard Michele T MT

The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society 20191112 1

Hyaluronan (HA) is a ubiquitous component of the extracellular matrix. The spatial-temporal localization of HA can be visualized in situ using biotinylated HA binding proteins (HABPs). This assay is sensitive to fixation conditions, and there are currently no best practices for HA detection. Thus, the goal of this study was to optimize fixation conditions for visualizing HA in the ovary, kidney, and liver through analysis of six commonly used fixatives for HA detection: Bouin's Solution, Carnoy' ...[more]

PMID: 31714169

Similar Datasets

Project description:BackgroundLigand-based virtual screening plays a fundamental part in the early drug discovery stage. In a virtual screening, a chemical library is searched for molecules with similar properties to a query molecule by means of a similarity function. The optimal assignment of chemical graphs has proven to be a valuable similarity function for many cheminformatic tasks, such as virtual screening. The optimal assignment assumes all atoms of a query molecule to be equally important, which is not realistic depending on the binding mode of a ligand. The importance of a query molecule's atoms can be integrated in the optimal assignment by weighting the assignment edges. We optimized the edge weights with respect to the virtual screening performance by means of evolutionary algorithms. Furthermore, we propose a visualization approach for the interpretation of the edge weights.ResultsWe evaluated two different evolutionary algorithms, differential evolution and particle swarm optimization, for their suitability for optimizing the assignment edge weights. The results showed that both optimization methods are suited to optimize the edge weights. Furthermore, we compared our approach to the optimal assignment with equal edge weights and two literature similarity functions on a subset of the Directory of Useful Decoys using sophisticated virtual screening performance metrics. Our approach achieved a considerably better overall and early enrichment performance. The visualization of the edge weights enables the identification of substructures that are important for a good retrieval of ligands and for the binding to the protein target.ConclusionsThe optimization of the edge weights in optimal assignment methods is a valuable approach for ligand-based virtual screening experiments. The approach can be applied to any similarity function that employs the optimal assignment method, which includes a variety of similarity measures that have proven to be valuable in various cheminformatic tasks. The proposed visualization helps to get a better understanding of the binding mode of the analyzed query molecule.

Project description:Modern histopathology is built on the cornerstone principle of tissue fixation, however there are currently no analytical methods of detecting fixation and as a result, in clinical practice fixation is highly variable and a persistent source of error. We have previously shown that immersion in cold formalin followed by heated formalin is beneficial for preservation of histomorphology and have combined two-temperature fixation with ultra-sensitive acoustic monitoring technology that can actively detect formalin diffusing into a tissue. Here we expand on our previous work by developing a predictive statistical model to determine when a tissue is properly diffused based on the real-time acoustic signal. We trained the model based on the morphology and characteristic diffusion curves of 30 tonsil cores. To test our model, a set of 87 different tonsil samples were fixed with four different protocols: dynamic fixation according to our predictive algorithm (C/H:Dynamic, N = 18), gold-standard 24 hour room temperature (RT:24hr, N = 24), 6 hours in cold formalin followed by 1 hour in heated formalin (C/H:6+1, N = 21), and 2 hours in cold formalin followed by 1 hour in heated formalin (C/H:2+1, N = 24). Digital pathology analysis revealed that the C/H:Dynamic samples had FOXP3 staining that was spatially uniform and statistically equivalent to RT:24hr and C/H:6+1 fixation protocols. For comparison, the intentionally underfixed C/H:2+1 samples had significantly suppressed FOXP3 staining (p<0.002). Furthermore, our dynamic fixation protocol produced bcl-2 staining concordant with standard fixation techniques. The dynamically fixed samples were on average only submerged in cold formalin for 4.2 hours, representing a significant workflow improvement. We have successfully demonstrated a first-of-its-kind analytical method to assess the quality of fixation in real-time and have confirmed its performance with quantitative analysis of downstream staining. This innovative technology could be used to ensure high-quality and standardized staining as part of an expedited and fully documented preanalytical workflow.

Dataset Information

Tissue-specific Fixation Methods Are Required for Optimal In Situ Visualization of Hyaluronan in the Ovary, Kidney, and Liver.

Publications

Tissue-specific Fixation Methods Are Required for Optimal In Situ Visualization of Hyaluronan in the Ovary, Kidney, and Liver.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets