Biology subjects

Tsai, J. W.

Publications and source records attributed to Tsai, J. W..

5 recordsLinked to original sources

bioRxiv2026

Phenotypic screens identify biologic regulators of nanoparticle uptake in diffuse midline glioma

Nanoparticle drug delivery systems hold considerable promise for locoregional administration to central nervous system tumors, yet the biological determinants of nanoparticle-cancer cell interactions remain poorly understood. Using patient-derived histone-mutant diffuse midline glioma (DMG) models, we performed a pooled CRISPR-Cas9 perturbation screen to systematically identify regulators of liposomal nanoparticle delivery. The screen identified candidate genes spanning endocytosis, vesicle transport, and metabolic signaling, revealing that nanoparticle delivery is governed by a broader landscape than previously appreciated. Among these, CTNNB1, or {beta}-catenin, emerged as a common negative regulator across two independent DMG models and two distinct nanoparticle surface chemistries. Transcriptomic profiling of CTNNB1-depleted DMG cells revealed upregulation of membrane remodeling and extracellular matrix gene programs, accompanied by reduced cell stiffness measured by a microfluidic acoustic scattering assay. This resulted in a shift in endocytic activity characterized by decreased bulk-phase macropinocytosis and increased receptor-mediated endocytosis. We further identified MAPK and mTOR pathway members as nanoparticle trafficking modulators, and demonstrated concordance between genetic and pharmacologic perturbations in modulating the liposomal nanoparticle interactions in pediatric DMG cells. These findings establish a biology-first screening approach for identifying previously unappreciated regulators with potential relevance to nanoparticle-based therapeutic strategies in pediatric brain tumors.

bioengineering↗

bioRxiv2025

Protocol for Seahorse 3D Mito Stress assay in patient-derived pediatric brain tumor single neurospheres

Metabolism is essential for cellular functions and is often altered in cancer. While Seahorse assays are well established for measuring metabolic changes in 2D cell cultures, their application to 3D models remains challenging. Here, we present a step-by-step protocol for plating individual brain tumor neurospheres in the assay microplate to measure their bioenergetics. We provide actionable recommendations and highlight pitfalls to avoid. This approach enables exploration of dynamic metabolic changes in patient-derived brain tumor neurospheres following genetic or pharmacologic interventions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/691986v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@25cb34org.highwire.dtl.DTLVardef@13ff857org.highwire.dtl.DTLVardef@c91c7forg.highwire.dtl.DTLVardef@16dfa27_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIOptimization of Seahorse assay protocol for single patient-derived brain tumor spheroids C_LIO_LIStep-by-step instructions for successfully re-plating and transferring single brain tumor spheroids C_LIO_LIImportance of microplate coating for the successful execution of Seahorse assays C_LIO_LIImaging of the microplate before and after the assay allows for normalization of metabolic parameters based on neurosphere size C_LI

cell biology↗

bioRxiv2023

Cell lineage analysis with somatic mutations reveals late divergence of neuronal cell types and cortical areas in human cerebral cortex

The mammalian cerebral cortex shows functional specialization into regions with distinct neuronal compositions, most strikingly in the human brain, but little is known in about how cellular lineages shape cortical regional variation and neuronal cell types during development. Here, we use somatic single nucleotide variants (sSNVs) to map lineages of neuronal sub-types and cortical regions. Early-occurring sSNVs rarely respect Brodmann area (BA) borders, while late-occurring sSNVs mark neuron-generating clones with modest regional restriction, though descendants often dispersed into neighboring BAs. Nevertheless, in visual cortex, BA17 contains 30-70% more sSNVs compared to the neighboring BA18, with clones across the BA17/18 border distributed asymmetrically and thus displaying different cortex-wide dispersion patterns. Moreover, we find that excitatory neuron-generating clones with modest regional restriction consistently share low-mosaic sSNVs with some inhibitory neurons, suggesting significant co-generation of excitatory and some inhibitory neurons in the dorsal cortex. Our analysis reveals human-specific cortical cell lineage patterns, with both regional inhomogeneities in progenitor proliferation and late divergence of excitatory/inhibitory lineages.

neuroscience↗

bioRxiv2020

Evolving Structure and Diversity of Human Narratives in the Journal of Stories in Science

Fundamentally, science is about people. The stories of the people behind the science are just as important as the results themselves, even though the results are often what get more attention. Despite the growth of databases storing such stories across diverse mediums, a detailed assessment of those databases is missing. To continue innovating science storytelling, we provide the first assessment of the structure and diversity of the narratives published in the Journal of Stories in Science. In this assessment, a total of 170 published stories authored by 158 authors between 2016 and 2020 are analyzed. Majority (67%) of the authors are women from North America and in the life sciences. The narratives most commonly feature authors from academia (e.g., 23% graduate students, 13% post-doctoral fellows and 21% professors). However, there is also a growing number of authors with PhDs that are working outside of academia (15%). Nearly a quarter (23%) of the database authors come from racial groups (African American, Latino, and Hispanic) that have been shown to be underrepresented in health-related sciences in the United States. Using the industry standard Flesch Reading Ease Score, we found that 74% of the stories included in the analysis fall in the target range of 50-70, which represents readability by students in grades 8-12. The analysis here provides the first deep look into one of the databases publishing diverse stories in science using a wide range of mediums. In summary, there is a need for more emphasis on both expanding and studying such databases given the continuous demand for these stories and their inclusion into K-12 curriculums.

scientific communication and education↗

bioRxiv2020

Melanopsin-dependent direct photic effects are equal to clock-driven effects in shaping the nychthemeral sleep-wake cycle

Nychthemeral sleep-wake cycles (SWc) are known to be generated by the circadian clock in suprachiasmatic nuclei (SCN), entrained to the light-dark cycle. Light also exerts direct acute effects on sleep and waking. However, under longer photic exposure such as the 24-hour day, the precise significance of sustained direct light effects (SDLE) and circuitry involved have been neither clarified nor quantified, as disentangling them from circadian influence is difficult. Recording sleep in mice lacking a circadian pacemaker and/or melanopsin-based phototransduction, we uncovered, contrary to prevailing assumptions, that circadian-driven input shapes only half of SWc, with SDLE being equally important. SDLE were primarily mediated (>80%) through melanopsin, of which half were relayed through SCN, independent of clock function. These findings were used for a model that predicted SWc under simulated jet-lag, and revealed SDLE as a crucial mechanism influencing behavior, and should be considered for circadian/sleep disorder management and societal lighting optimization.

neuroscience↗