Biology subjects

Otero, J. J.

Publications and source records attributed to Otero, J. J..

3 recordsLinked to original sources

bioRxiv2026

Intra-slide calibration technology improves immunohistochemical harmonization within and between anatomic pathology laboratories

The reproducibility of immunohistochemistry in tumor tissue analysis across reference labs remains a persistent challenge. We tested the extent to which an intra-slide calibration technology mitigated discprepencies in inter-laboratory assays of p53 immunohistochemical (IHC) reactions in brain biopsies of glioblastoma (GB), IDH-wildtype. Intra-slide calibration technologies apply a 0-100% concentration scale incorporating primary surrogate and secondary antibodies to generate a standardized curve for DAB precipitation. IHC from GB samples was performed independently by pathology departments from two different hospital laboratories and were digitalized at 40x magnification using Aperio Image Scope software. Feature extraction, including intensity and texture parameters was performed using the EBImage package in R, followed by UMAP dimensionality reduction and DBSCAN clustering analysis. Our results show significant differences in intensity and texture clustering patterns between laboratory tissue samples and intra-slide calibration technology ruler caused by the different laboratories. Intra-slide calibration technology coupled with polynomial regression analysis improved ~90% the data harmonization. Our findings demonstrate a key role for computational pathology using intra-slide calibration technology to enable intra-laboratory consistency and inter-laboratory reproducibility. These advances strengthen the reproducibility of diagnostic assessments and support more objective, data-driven decision-making in neuro-oncology.

bioinformatics↗

bioRxiv2022

DNA-caged Nanoparticles via Electrostatic Self-Assembly

DNA-modified nanoparticles enable DNA sensing and therapeutics in nanomedicine and are also crucial for nanoparticle self-assembly with DNA-based materials. However, methods to conjugate DNA to nanoparticle surfaces are limited, inefficient, and lack control. Inspired by DNA tile nanotechnology, we demonstrate a new approach to nanoparticle modification based on electrostatic attraction between negatively charged DNA tiles and positively charged nanoparticles. This approach does not disrupt nanoparticle surfaces and leverages the programmability of DNA nanotechnology to control DNA presentation. We demonstrated this approach using a variety of nanoparticles, including polymeric micelles, polystyrene beads, gold nanoparticles, and superparamagnetic iron oxide nanoparticles with sizes ranging from 5-20 nm in diameter. DNA cage formation was confirmed through transmission electron microscopy (TEM), neutralization of zeta potential, and a series of fluorescence experiments. DNA cages present "handle" sequences that can be used for reversible target attachment or self-assembly. Handle functionality was verified in solution, at the solid-liquid interface, and inside fixed cells, corresponding to applications in biosensing, DNA microarrays, and erasable immunocytochemistry. These experiments demonstrate the versatility of the electrostatic DNA caging approach and provide a new pathway to nanoparticle modification with DNA that will empower further applications of these materials in medicine and materials science.

bioengineering↗

bioRxiv2021

Phox2b mutation mediated by Atoh1 expression impaired respiratory rhythm and ventilatory responses to hypoxia and hypercapnia

Retrotrapezoid nucleus (RTN) neurons are involved in central chemoreception and respiratory control. Lineage tracing studies demonstrate RTN neurons to be derived from Phox2b and Atoh1 expressing progenitor cells in rhombere 4. Phox2b exon 3 mutations cause congenital central hypoventilation syndrome (CCHS), producing an impaired respiratory response to hypercapnia and hypoxia. Our goal was to investigate the extent to which a conditional mutation of Phox2b within Atoh1-derived cells might affect a) respiratory rhythm; b) ventilatory responses to hypercapnia and hypoxia and c) number of RTN-chemosensitive neurons. Here, we used a transgenic mouse line carrying a conditional Phox2b{Delta}8 mutation activated by cre-recombinase. We crossed them with Atoh1Cre mice. Ventilation was measured by whole body plethysmograph during neonate and adult life. In room air, experimental and control groups showed similar basal ventilation; however, Atoh1Cre/Phox2b{Delta}8 increased breath irregularity. The hypercapnia and hypoxia ventilatory responses were impaired in neonates. In contrast, adult mice recovered ventilatory response to hypercapnia, but not to hypoxia. Anatomically, we observed a reduction of the Phox2b+/TH- expressing neurons within the RTN region. Our data indicates that conditionally expression of Phox2b mutation by Atoh1 affect development of the RTN neurons and are essential for the activation of breathing under hypoxic and hypercapnia condition, providing new evidence for mechanisms related to CCHS neuropathology.

neuroscience↗