Biology subjects

Villasenor, R.

Publications and source records attributed to Villasenor, R..

6 recordsLinked to original sources

bioRxiv2026

Integrin-dependent trafficking of CD98hc reduces endocytic noise to maintain metabolic homeostasis

A stable supply of amino acids is essential for cellular homeostasis. CD98hc is an indispensable component of the LAT1 amino acid transporter. Here, we found an unexpected role for {beta}1-integrin in amino acid homeostasis via the regulation of CD98hc trafficking. We identified Fast Endophilin-Mediated Endocytosis (FEME) as the primary internalization route for CD98hc in both osteosarcoma and brain endothelial cells. Endocytosis was followed by {beta}1-integrin-dependent recycling, which diverted CD98hc from early endosomes. By combining mathematical modelling with high-content imaging, we demonstrate that this trafficking pathway exhibited emergent properties that filtered high-frequency endocytic events to stabilize CD98hc at the plasma membrane. Mutating CD98hc to disrupt its interaction with {beta}1-integrin led to redistribution of the transporter into early endosomes, reduced intracellular amino acid levels and impaired growth under metabolic stress. We propose that regulation of transporter trafficking dynamics is a general mechanism to buffer endocytic noise and maintain metabolic homeostasis.

cell biology↗

bioRxiv2026

Proximity labeling at H3K9me3 reveals VRK-1 regulate global chromatin distribution in C. elegans

Heterochromatin marked by histone H3 lysine 9 di- or trimethylation (H3K9me2/3) underpins transcriptional silencing and nuclear organization, yet its full complement of associated proteins remains incompletely defined. Here, we apply ChromID proximity labelling with the mouse HP1{beta} chromodomains to map the H3K9me3-proximal proteome in Caenorhabditis elegans, recovering known heterochromatin factors alongside previously uncharacterized candidates. We pursued one such candidate, the vaccinia-related kinase VRK-1, because of its established but poorly understood links to chromatin organization. Intriguingly, VRK-1 dynamically relocates from a broad nuclear distribution to the nuclear periphery upon azide or heat stress. Following these stresses, bulk chromatin exhibits similarly increased peripheral enrichment and apparent compaction, as assessed by radial fluorescence profiles. Although VRK-1 is not necessary for stress-induced chromatin reorganization, decompaction and repositioning of chromatin away from the nuclear envelope during recovery requires VRK-1. VRK-1 depletion leads to persistent perinuclear chromatin retention and compromises post-stress survival. Furthermore, loss of VRK-1 catalytic activity results in over-retention of chromatin at the nuclear periphery under normal growth conditions; this phenotype can be reversed by depletion of a key VRK-1 substrate at the nuclear envelope BAF-1. Our findings identify VRK-1 as a key regulator that controls the interaction of chromatin with the nuclear lamina through regulation of BAF-1.

cell biology↗

bioRxiv2025

A modular toolbox for in cellulo screening of small molecule inhibitors targeting chromatin reader domains

The dysregulation of bromodomain proteins, a family of "reader" proteins that recognize the critical post-translational modification of acylation, is implicated in diseases like cancer, making them important therapeutic targets. However, the development of specific small-molecule inhibitors is hindered by the lack of robust, high-throughput cellular assays to measure target engagement and off-target binding in living cells. To address this gap, we developed a modular platform of cell lines that stably express synthetic chromatin reader constructs, termed Acyl-eCRs, containing various bromodomains fused to eGFP. We demonstrate that these Acyl-eCRs recapitulate the same response to bromodomain inhibitors and PROTACs as endogenous proteins, allowing for the quantitative assessment of drug effects. We introduce two complementary flow cytometry-based assays to evaluate inhibitor-target engagement: a competitive binding assay leveraging PROTAC-induced degradation, and a nuclear retention assay that directly measures the displacement of bromodomains from chromatin. Our approach circumvents the need for laborious protein purification and in vitro characterization, providing a scalable and physiologically relevant method for assessing inhibitor potency and specificity. This platform represents a versatile tool for chemical biology, enabling the functional evaluation of chromatin-targeting drugs in a native cellular context.

molecular biology↗

bioRxiv2024

A CRISPR/Cas9 screen reveals proteins at the endosome-Golgi interface that modulate cellular ASO activity

Anti-sense oligonucleotides (ASOs) are modified synthetic single-stranded molecules with enhanced stability, activity, and bioavailability. They associate with RNA through sequence complementarity and can reduce or alter mRNA expression upon binding of splice site positions. To target RNA in the nucleus or cytoplasm, ASOs must cross membranes, a poorly understood process. We have performed an unbiased CRISPR/Cas9 knockout screen with a genetic splice reporter to identify genes that can increase or decrease ASOs activity, resulting in the most comprehensive catalog of ASOs-activity modifier genes. Distinct targets were uncovered, including AP1M1 and TBC1D23, linking ASOs activity to transport of cargo between the Golgi and endosomes. AP1M1 absence strongly increased ASO activity by delaying endosome-to-lysosome transport in vitro and in vivo. Prolonged ASOs residence time in the endosomal system may increase the likelihood of ASOs escape from this organelle before they reach lysosomes. This insight into AP1M1 role in ASOs trafficking suggests a way for enhancing the therapeutic efficacy of ASOs by manipulating the endolysosomal pathways.

cell biology↗

bioRxiv2024

Advanced Tissue Technologies of Blood-Brain Barrier Organoids as High Throughput Toxicity Readouts in Drug Development

Recent advancements in engineering Complex in vitro models (CIVMs) such as Blood-brain barrier (BBB) organoids offer promising platforms for preclinical drug testing. However, their application in drug development, and especially for the regulatory purposes of toxicity assessment, requires robust and reproducible techniques. Here, we developed an adapted set of orthogonal image-based tissue methods including hematoxylin and eosin staining (HE), immunohistochemistry (IHC), multiplex immunofluorescence (mIF), and Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) to validate CIVMs for drug toxicity assessments. We developed an artificial intelligence (AI) algorithm to increase the throughput and the reliability of histomorphologic evaluations of apoptosis for in vitro toxicity studies. Our data highlight the potential to integrate advanced morphology-based readouts such as histological techniques and digital pathology algorithms for use on CIVMs, as part of a standard preclinical drug development assessment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/611987v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@190530eorg.highwire.dtl.DTLVardef@3cce5forg.highwire.dtl.DTLVardef@10ec3borg.highwire.dtl.DTLVardef@1051585_HPS_FORMAT_FIGEXP M_FIG C_FIG The graphical abstract was partially created with biorender.com. HighlightsO_LIAdvanced Complex in vitro models (CIVMs) like Blood-brain barrier (BBB) organoids show promise for preclinical drug testing. However, robust and reproducible techniques are crucial for the acceptance of CIVMs in drug development processes, especially for toxicity assessments which are highly regulated by health authorities. C_LIO_LIWe developed orthogonal image-based readouts on histological sections to enable the use of BBB organoids for future compound toxicity assessment. C_LIO_LIA newly established artificial intelligence (AI) algorithm provides automated and label-free detection of apoptotic cells in drug screening using BBB organoids and provides an alternative killing assay on single cell resolution (40x) to current standards. C_LI

pathology↗

bioRxiv2024

ApoE4 disrupts intracellular trafficking and iron homeostasis in an improved iPSC-based model of human brain endothelial cells

Transferrin receptor in brain endothelial cells can deliver therapeutic antibodies to the brain via transcytosis across the blood-brain barrier. Whether receptor transport remains intact in Alzheimers disease is still a major open question. Here, we investigated whether apolipoprotein E4 (ApoE4), the major genetic risk factor for Alzheimers disease, altered intracellular transport in human brain endothelial cells. To achieve this, we first developed an optimized protocol for induced pluripotent stem cells based on a defined chemical cocktail and extracellular-matrix support to differentiate brain endothelial cells (iCE-BECs). Multi-omic profiling and functional transport assays showed that iCE-BECs have a brain endothelial gene signature and recapitulate receptor-mediated transcytosis of a clinically validated BrainshuttleTM antibody against transferrin receptor. Engineered iCE-BECs homozygous for ApoE4 had altered spatiotemporal organization of early endosomes, increased transferrin receptor expression and reduced cytoplasmic iron. Our data revealed that ApoE4 can impact intracellular transport and iron homeostasis at the BBB in a cell-autonomous manner. This finding could be relevant for the brain delivery of therapeutic antibodies for Alzheimers disease.

cell biology↗