Biology subjects

park, j.

Publications and source records attributed to park, j..

3 recordsLinked to original sources

bioRxiv2026

Label-Free 4D Holotomography with Depth-Adaptive Segmentation for Quantitative Analysis of Lipid Droplet Dynamics in Hepatic Organoids

SignificanceQuantifying lipid droplet (LD) remodeling in 3D hepatic organoids is often limited to endpoint staining or phototoxic live fluorescence imaging, thereby obscuring droplet-level kinetics. AimWe aimed to develop a label-free method to track LD dynamics in living hepatic organoids under different fatty-acid loads. ApproachTime-lapse 3D refractive-index tomograms were acquired using holotomography and analyzed with a depth-adaptive, multi-threshold segmentation pipeline to quantify LD number, volume, sphericity, and refractive-index-derived concentration and dry mass at single-droplet resolution. ResultsOleic acid and linoleic acid induced LD accumulation while preserving organoid integrity, whereas palmitic acid triggered rapid structural collapse. Despite increases in total LD burden under both oleic acid and linoleic acid, droplet-level dynamics diverged: oleic acid produced volume-dominated accumulation via enlargement of fewer LDs and increased size heterogeneity, whereas linoleic acid produced number-dominated accumulation via sustained increases in LD number, yielding a more uniform population of small droplets. ConclusionsLabel-free holotomography with depth-adaptive analysis enables non-invasive, longitudinal, and multi-scale quantification of LD dynamics in intact organoids and reveals fatty-acid- dependent temporal modes of lipid storage. Statement of DiscoveryWe developed a label-free, longitudinal 3D holotomography framework with depth-adaptive lipid droplet segmentation that quantifies single-droplet dynamics in living mouse hepatic organoids. Using this platform, we found that oleic acid and linoleic acid induce LD accumulation via distinct strategies--oleic acid via droplet enlargement and linoleic acid via sustained increases in droplet number--while palmitic acid rapidly compromises organoid integrity.

biophysics↗

bioRxiv2025

Label-free classification of cell death pathways via holotomography-based deep learning framework

Accurate classification of cell death pathways is critical in understanding disease mechanisms and evaluating therapeutic responses, as dysregulated cell death underlies a wide range of pathological conditions including cancer and therapy resistance. Conventional imaging methods such as fluorescence and bright-field microscopy, or 2D phase imaging, often suffer from phototoxicity, labeling artifacts, or limited morphological contrast. Here, we present a real-time, label-free platform for classifying cell death phenotypes--apoptosis, necroptosis, and necrosis--by combining three-dimensional holotomography with deep learning. Our convolutional neural network, trained on refractive index (RI)-based features from HeLa cells, achieved high classification accuracy (97.2 {+/-} 2.8%) under varying cell densities. Notably, the model identified early RI changes during necroptosis several hours prior to fluorescence-based markers. These findings demonstrate the potential of holotomography-based AI for high-resolution, label-free cell death profiling.

cell biology↗

bioRxiv2023

Interplay between Nrf2 and αB-crystallin in the lens and heart of zebrafish under proteostatic stress

A coordinated oxidative stress response, partly triggered by the transcription factor Nrf2, protects cells from the continual production of reactive oxygen species. Left unbuffered, reactive oxygen species can lead to protein aggregation which has been implicated in a spectrum of diseases including cataract of the ocular lens and myopathy of the heart. While proteostasis is maintained by diverse families of heat shock proteins, the interplay between the oxidative and proteostatic stress responses in the lens and the heart have not been investigated. Capitalizing on multiple zebrafish lines that have compromised function of Nrf2 and/or the two zebrafish small heat-shock proteins Ba- and Bb-crystallin, we uncovered a transcriptional relationship that leads to a substantial increase in Bb-crystallin transcripts in the heart in response to compromised function of Nrf2. In the lens, the concomitant loss of function of Nrf2 and Ba-crystallin leads to upregulation of the cholesterol biosynthesis pathway thus mitigating the phenotypic consequences of the Ba-crystallin knockout. In contrast, abrogation of Nrf2 function accentuates the penetrance of a heart edema phenotype characteristic of embryos of B-crystallin knockout lines. Multiple molecular pathways, such as genes involved in extracellular interactions and implicated in cardiomyopathy, are revealed from transcriptome profiling thus identifying novel targets for further investigation. Together our transcriptome/phenotypic analysis establishes an intersection between the oxidative stress and chaperone responses in the lens and the heart.

molecular biology↗