Biology subjects

Huynh, L.

Publications and source records attributed to Huynh, L..

15 recordsLinked to original sources

bioRxiv2026

CRTC, not phosphorylated CREB1, drives cAMP-induced transcription across diverse cell types

Specialized cell types layer cell-type-restricted proteins, metabolites, and organelles onto a shared foundation of core cellular processes. How this ubiquitous machinery generates lineage-specific outputs is central to both cell biology and therapeutic development. G-protein-coupled receptors (GPCRs) respond to receptor-restricted ligands to drive cell-type-specific transcription through cAMP-mediated activation of protein kinase A (PKA), which activates the transcription factor CREB1 through two parallel modes: direct phosphorylation at serine 133, and inhibition of salt-inducible kinases (SIK) that restrain the CRTC coactivators. How these modes integrate and contribute to signaling across cell types has remained unresolved, obscured by genetic redundancy and essentiality. Here we combine focused genetic analyses with a cross-lineage transcriptomic survey to dissect these parallel inputs. In Creb1/Atf1/Crem triple-knockout cells, a non-phosphorylatable mutant CREB1S133A fully rescued endogenous target gene activation, while Crtc1/Crtc2/Crtc3 ablation abolished transcription even with intact CREB1 serine 133 phosphorylation. As part of this mechanism, we found the annotated repressor ICER can instead act as a positive regulator, substituting for full-length CREB1 paralogs to drive a feedforward loop. Across melanocytes, hepatocytes, osteocytes, macrophages, and neurons, SIK inhibition recapitulated cAMP-PKA-driven transcription across both shared and cell-type-specific gene expression programs, with neurons a notable exception. These results invert the canonical model, placing CRTC recruitment as the dominant driver of CREB1-mediated transcription across diverse lineages, reframing how cAMP-PKA signaling can be interpreted and therapeutically targeted.

cell biology↗

bioRxiv2026

A genetic screen unveils the polymerization cycle of the bacterial actin-like MreB

MreB, a bacterial actin homolog and polymerizing ATPase, is central to cell-shape maintenance and cell-wall integrity. Its functions rely on its ability to assemble into dynamic, membrane-associated polymers. However, how nucleotide binding and hydrolysis, MreB-MreB contacts, and membrane association are coordinated to enable polymer assembly and disassembly remains unclear. Here, we combined genetics and live-cell microscopy with biochemical approaches to dissect these processes. Using a highly sensitive reporter of MreB activity, we identified, through a genetic screen, residues critical for MreB function in Bacillus subtilis. Subsequent extensive characterization of corresponding stable variants of the homologous Geobacillus stearothermophilus MreB revealed that ATP binding, but not ATP hydrolysis, is required for polymerization. Productive longitudinal intraprotofilament contacts are required for efficient ATP hydrolysis and enhance membrane association. Perturbations predicted to weaken lateral interprotofilament contacts altered membrane association and modulated ATPase activity. Together, these effects provide experimental evidence consistent with long-range functional coupling among the longitudinal and lateral protofilament interfaces, the distant nucleotide-binding site, and membrane association dynamics. Moreover, impaired ATP hydrolysis delays disassembly of lipid-associated polymers, indicating that hydrolysis promotes polymer turnover. These results establish key mechanistic steps coordinating ATP-driven MreB polymerization and turnover and provide a basis for a complete MreB assembly-disassembly cycle and for further elucidating how MreB dynamics contribute to cell-wall organization.

microbiology↗

bioRxiv2026

Impact of temperature on patient-derived dengue virus breakthrough infections in wMel-infected Aedes aegypti.

The wMel strain of the insect endosymbiont Wolbachia reduces the potential for Aedes aegypti to transmit mosquito-borne viruses such as dengue (DENV). Field trials that have introgressed wMel into Ae. aegypti populations have shown this approach significantly reduces dengue incidence. In a laboratory setting some wMel-Ae. aegypti develop infectious saliva following a viremic blood meal. Additionally, studies have demonstrated that exposing wMel-Ae. aegypti to heat treatment, particularly during the larval stage, reduces wMel density in key tissues such as the ovaries, midgut and salivary glands. Here we build on these studies, using viremic blood collected from 13 dengue inpatients at the Hospital for Tropical Diseases in Ho Chi Minh City (Viet Nam), to assess how temperature affects the protection afforded to Ae. aegypti by wMel. We found that, compared to wMel-Ae. aegypti reared at 28 {+/-} 4{degrees}C, those reared at 31 {+/-} 4{degrees}C developed infectious saliva more frequently, but the risk of this occurring was still reduced compared to WT mosquitoes reared at the same temperature. Heat treatment reduced the density of wMel in all tissues tested, decreased the magnitude of wMels protection against DENV replication in the head/thorax, and significantly increased the amount of DENV replication in wMel-Ae. aegypti. When comparing cohorts of wMel-Ae. aegypti that did or did not develop infectious saliva, DENV levels in the head/thorax were associated with increased odds of mosquitoes developing infectious saliva, but wMel density was not. Overall, these findings show that elevated rearing temperatures increase the risk of patient-derived DENV breakthrough infections in wMel-Ae. aegypti, potentially due to increased DENV replication in these mosquitoes. This limitation suggests it would be prudent to increase surveillance in regions using wMel for dengue control when daily mean temperatures remain above 30{degrees}C for multiday periods. Author SummaryThe mosquito species Ae. aegypti can be infected with the bacterium Wolbachia (wMel strain), reducing its capacity to transmit viruses like dengue (DENV). Wolbachia is now being used as a biocontrol tool to reduce the burden of dengue in communities. However, some mosquitoes with Wolbachia can still transmit DENV. Here we utilised a natural infection model using dengue patient-derived blood to examine how temperature may increase the risk of DENV transmission occurrence in mosquitoes with wMel. Mosquitoes with wMel were more likely to transmit virus when reared at an average temperature of 31{degrees}C compared to those reared at an average temperature of 28{degrees}C but these mosquitoes still had a lower risk of developing infectious saliva compared to their wMel-free counterparts. Higher temperatures reduced the amount of wMel in mosquito tissues and increased the amount of DENV replicating in the head/thorax. Increasing levels of DENV RNA in these tissues were found to be associated with increased risk of mosquitoes with wMel developing infectious saliva. This finding indicates surveillance is warranted in high temperature settings or during heat waves, to monitor for changes in wMel frequency and DENV infection in Ae. aegypti.

microbiology↗

bioRxiv2026

ImmTACs overcome cytotoxic T cell suppression

Immune mobilizing monoclonal TCR against cancer (ImmTAC) are cancer therapeutics that activate T cells through recognition of a tumor-associated antigenic MHC/peptide complex. A first-in-class ImmTAC, Tebentafusp, is approved for the treatment of metastatic uveal melanoma. While clinical efficacy is thus established, the cellular mechanisms underpinning ImmTAC action are not fully resolved. Using a recently established experimental strategy to generate suppressed human primary cytotoxic T lymphocytes (CTL), we have investigated an ImmTAC that recognizes a peptide derived from the tumor associated antigen NY-ESO-1 in comparison to direct engagement of a TCR recognizing the same MHC/peptide complex. In response to endogenous antigen presentation, ImmTACs could elicit tumor cell cytolysis by suppressed CTL, but not IFN{gamma} secretion, in a manner dependent on the engager affinity for CD3{varepsilon}. ImmTACs enhanced the efficient execution of subcellular CTL polarization steps required for effective cytolysis and could trigger calcium signaling. These data establish that ImmTACs activate CTL similarly to direct engagement of a TCR by MHC/peptide and are likely to retain this capability under suppressive conditions such as in the tumor microenvironment.

immunology↗

bioRxiv2025

Slow trajectories generate divergent cell fates following antibiotic stress

Single-cell microfluidic experiments have shown that upon abrupt exposures to antibiotics, genetically homogeneous microbial populations undergo divergent cell fates. The mechanism underlying this divergence is not clear and in particular, the emergence of a range of distinct slow-growing phenotypes cannot be explained by models relying on bistability alone. Here, we propose a model for gene expression and growth dynamics during antibiotic exposures, which is informed by well-known scaling relations connecting proteome allocation and cell growth. In our model, resources available for transcription and translation of resistance genes act like generalized momenta and their initial variation is predictive of cell fate. Our model reproduces key experimental observations, including the prediction of specific phenotypes and a critical threshold in initial resource allocation that predicts cell survival. These results offer an alternative mechanism for the emergence of phenotypic diversity where slow cell growth effectively stabilizes cellular states along the trajectory that are far from the final stable states predicted by fixed points.

microbiology↗

bioRxiv2025

Caenorhabditis elegans Uses Canonical and Non-canonical Hippo signaling

Hippo signaling is a conserved regulator of tissue homeostasis across metazoans. The Ste20 family kinase Hippo/MST activates the NDR family kinase Warts/LATS to inhibit the transcriptional coactivator Yorkie/YAP/TAZ and its transcription factor partner Scalloped/TEAD. In Caenorhabditis elegans, cell lineages and organ sizes are largely invariant, and classical Hippo phenotypes such as tissue overgrowth are absent. Nevertheless, WTS-1, YAP-1, and the TEAD-like transcription factor EGL-44 form a conserved core module required for larval development past the L2 stage. Crucially, a direct role for Hippo signaling remains unestablished. To address this question, we generated a fluorescently tagged endogenous YAP-1 as a live biomarker of pathway activity. Upon WTS-1 loss, endogenous YAP-1 translocated from cytosol to nucleus in epithelium and intestine. Tissue-specific depletion revealed that intestinal, but not epithelial, WTS-1 is essential for progression past L2. The duplicated Hippo-related kinases CST-1 and CST-2 repressed YAP-1 nuclear localization in the epithelium but not intestine, indicating that intestinal WTS-1 functions without CST-1/2. The Ste20 kinase MIG-15, orthologous to Drosophila Misshapen and mammalian MAP4K4/6/7/8, was redundant with CST-1/2 for larval progression. Yet deficient MIG-15 uniquely increased YAP-1 abundance without driving nuclear localization. By contrast, the Ste20 kinase GCK-2, orthologous to Drosophila Happyhour and mammalian MAP4K1/2/3/5, had no detectable role. Our findings establish C. elegans as a model for Hippo signaling, with a canonical cascade active in the epithelium and noncanonical inputs controlling WTS-1 in the intestine. In this context, YAP-1/EGL-44 outputs are repurposed from growth control to non-proliferative developmental functions.

developmental biology↗

bioRxiv2025

Interaction with tumor cell spheroids induces suppression in primary human cytotoxic T cells

Cytotoxic T lymphocytes (CTL) are key effectors in the anti-tumor immune response. However, their function is commonly suppressed in tumors in the form of exhausted CTL. Understanding molecular mechanisms of suppression and of therapeutics to overcome them is of substantial basic and translational importance yet hindered by limited access to large numbers of exhausted CTL in vitro. Here we use three-dimensional tissue culture to generate primary human CTL with suppressed function. Using a 21-antibody flow cytometry panel and determination of calcium signaling and cell couple maintenance, we show that these cells closely resemble exhausted CTL from tumors. For better understanding of in vitro human primary CTL as key tools in therapeutic development, before and after induction of suppression, we have determined the dependence of CTL function on technicalities of in vitro CTL generation, antigen dose and affinity across two T cell receptors and multiple tumor cell lines. We have investigated morphology and subcellular F-actin distributions of CTL as a key regulators of effector function. Primary human CTL formed cell couples with tumor target cells even in the absence of antigen. Yet, gradual stabilization of such cell couples was associated with increasing CTL effector function. Induction of suppression substantially destabilized CTL tumor cell couples. This comprehensive characterization of the phenotype of in vitro primary human CTL, including a suppressed state, should facilitate their wider use in basic and translational research.

immunology↗

bioRxiv2024

LINE1 promotes nuclear compartmentalization to repress the 8-cell state in embryonic stem cells

The family of LINE1 transposable elements underwent a massive expansion in mammalian genomes. While traditionally viewed as a mutagenic selfish element, recent studies point to roles for LINE1 in early mouse development, T cell quiescence and neurogenesis. Here we show that human LINE1 RNA is essential for self-renewal and identity of human embryonic stem cells (hESCs). Silencing of LINE1 using either antisense oligonucleotides or CRISPR interference in naive hESCs leads to a strong induction of 8C-like cells (8CLCs). We found that genes derepressed upon LINE1 KD are not uniformly distributed across the genome, with an enrichment for chromosome 19, which includes key markers of the 8C state such as TPRX1. Silencing of TPRX1, but not other putative 8C regulators p53 or H3.XY, suppresses the induction of the 8C program in LINE1 KD hESCs. We found that LINE1 RNA is preferentially localized to the lamina and periphery of the nucleolus in hESCs. Sequencing of Lamina-Associated Domains (LADs) and Nucleolus-Associated Domains (NADs) reveals a preferential association of chromosome 19 with NADs in hESCs. However, 8CLCs have a distinct nucleolar morphology and a lower association of chromosome 19 and TPRX1 loci with the nucleolus relative to naive and primed hESCs, suggesting a role for nucleolar dynamics in the 8CLC-hESC transition. In agreement, LINE1 KD leads to disruption of nucleolar architecture with signs of nucleolar stress. Independent perturbations of the nucleolus induce the 8C program in hESCs. Genes induced by LINE1 KD are enriched for targets of Polycomb Repressive Complex (PRC2), and inhibition of PRC2 leads to a strong induction of 8C genes. Our results indicate that LINE1 coordinates nuclear compartmentalization and chromatin-mediated gene repression to prevent developmental reversion of hESCs. HighlightsO_LIKnockdown of LINE1 induces TPRX1-dependent emergence of 8C-like cells in hESCs. C_LIO_LIGenes de-repressed upon LINE1 KD are enriched for Chr 19 and PRC2 targets. C_LIO_LI8CLCs display dissociation of Chromosome 19 from the nucleolus. C_LIO_LIDisruption of the nucleolus or inhibition of PRC2 strongly induce the 8C program. C_LI

developmental biology↗

bioRxiv2023

Five inhibitory receptors display distinct vesicular distributions in T cells

T cells can express multiple inhibitory receptors. Upon induction of T cell exhaustion in response to persistent antigen, prominently in the anti-tumor immune response, many are expressed simultaneously. Key inhibitory receptors are CTLA-4, PD-1, LAG3, TIM3 and TIGIT, as investigated here. These receptors are important as central therapeutic targets in cancer immunotherapy. Inhibitory receptors are not constitutively expressed on the cell surface, but substantial fractions reside in intracellular vesicular structures. It remains unresolved to which extent the subcellular localization of different inhibitory receptors is distinct. Using quantitative imaging of subcellular distributions and plasma membrane insertion as complemented by proximity proteomics and a biochemical analysis of the association of the inhibitory receptors with trafficking adaptors, the subcellular distributions of the five inhibitory receptors were discrete. The distribution of CTLA-4 was most distinct with preferential association with lysosomal-derived vesicles and the sorting nexin 1/2/5/6 transport machinery. With a lack of evidence for the existence of specific vesicle subtypes to explain divergent inhibitory receptor distributions, we suggest that such distributions are driven by divergent trafficking through an overlapping joint set of vesicular structures. This extensive characterization of the subcellular localization of five inhibitory receptors in relation to each other lays the foundation for the molecular investigation of their trafficking and its therapeutic exploitation.

immunology↗

bioRxiv2023

Epigenetic misactivation of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung cancer

Enhancer reprogramming has been proposed as a key source of transcriptional dysregulation during tumorigenesis, but the molecular mechanisms underlying this process remain unclear. Here, we identify an enhancer cluster required for normal development that is aberrantly activated in breast and lung carcinoma. Deletion of the SRR124-134 cluster disrupts transcription of the SOX2 oncogene and dysregulates genome-wide chromatin accessibility in cancer cells. Analysis of primary tumors reveals a correlation between chromatin accessibility at this cluster and SOX2 overexpression in breast and lung cancer patients. We demonstrate that FOXA1 is an activator and NFIB is a repressor of SRR124-134 activity and SOX2 transcription in cancer cells, revealing a co-opting of the regulatory mechanisms involved in early development. Notably, we show that the conserved SRR124 and SRR134 regions are essential during mouse development, where homozygous deletion results in the lethal failure of esophageal-tracheal separation. These findings provide insights into how developmental enhancers can be reprogrammed during tumorigenesis and underscore the importance of understanding enhancer dynamics during development and disease.

genomics↗

bioRxiv2022

ZO1 scaffold isoforms differentially contribute to electrical synapse formation

Electrical synapses are neuronal gap junction (GJ) channels associated with a macromolecular complex called the electrical synapse density (ESD), which regulates development and dynamically modifies electrical transmission. However, the proteomic makeup and molecular mechanisms utilized by the ESD that direct electrical synapse formation are not well understood. Using the Mauthner cell of zebrafish as a model, we previously found that the intracellular scaffolding protein ZO1b is a member of the ESD, localizing postsynaptically, where it is required for GJ channel localization, electrical communication, neural network function, and behavior. Here, we show that the complexity of the ESD is further diversified by the genomic structure of the ZO1b gene locus. The ZO1b gene is alternatively initiated at three transcriptional start sites resulting in isoforms with unique N-termini that we call ZO1b-Alpha, -Beta, and - Gamma. We demonstrate that ZO1b-Beta and ZO1b-Gamma are broadly expressed throughout the nervous system and localize to electrical synapses. By contrast, ZO1b-Alpha is expressed mainly non-neuronally and is not found at synapses. We generate mutants in all individual isoforms, as well as double mutant combinations in cis on individual chromosomes, and find that ZO1b-Beta is necessary and sufficient for robust GJ channel localization. ZO1b-Gamma, despite its localization to the synapse, plays an auxiliary role in channel localization. This study expands the notion of molecular complexity at the ESD, revealing that an individual genomic locus can contribute distinct isoforms to the macromolecular complex at electrical synapses. Further, independent scaffold isoforms have differential contributions to developmental assembly of the interneuronal GJ channels. We propose that ESD molecular complexity arises both from the diversity of unique genes and from distinct isoforms encoded by single genes. Overall, ESD proteomic diversity is expected to have critical impacts on the development, structure, function, and plasticity of electrical transmission.

neuroscience↗

bioRxiv2022

Inferring Density-Dependent Population Dynamics Mechanisms through Rate Disambiguation for Logistic Birth-Death Processes

Density dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can manifest in birth processes, death processes, or both. Therefore, we utilize the mean and variance of cell number fluctuations to separately identify birth and death rates from time series that follow stochastic birth-death processes with logistic growth. Our method provides a novel perspective on stochastic parameter identifiability, which we validate by analyzing the accuracy in terms of the discretization bin size. We apply our method to the scenario where a homogeneous cell population goes through three stages: (1) grows naturally to its carrying capacity, (2) is treated with a drug that reduces its carrying capacity, and (3) overcomes the drug effect to restore its original carrying capacity. In each stage, we disambiguate whether it happens through the birth process, death process, or some combination of the two, which contributes to understanding drug resistance mechanisms. In the case of limited data sets, we provide an alternative method based on maximum likelihood and solve a constrained nonlinear optimization problem to identify the most likely density dependence parameter for a given cell number time series. Our methods can be applied to other biological systems at different scales to disambiguate density-dependent mechanisms underlying the same net growth rate. Mathematics Subject Classifications60J27 {middle dot} 92D25 {middle dot} 62M10 {middle dot} 60J25

ecology↗

bioRxiv2021

Two Liberibacter Effectors Combine to Suppress Critical Innate Immune Defenses and Facilitate Huanglongbing Pathogenesis in Citrus

Genome sequence analyses predicted the presence of effectors in the gram-negative Candidatus Liberibacter asiaticus (CLas) even without the presence of a classical type III secretion system. Since CLas is not culturable, it is not possible to perform traditional gene knockout experiments to determine the role of various effectors in Huanglongbing (HLB) pathogenesis. Therefore, we followed an alternative functional genomics approach to examine the role of the CLas effectors in HLB pathogenesis in general and more specifically in suppressing citrus innate immune response. Here, we focused on the CLas effectors, P235 and Effector 3, to perform the following studies. First, proteomic studies by LC-MS/MS were conducted to screen the putative interacting citrus protein partners of P235 and Effector 3 from the healthy and CLas-infected Hamlin extracts and the most probable candidates were identified based upon their high protein scores from LC-MS/MS. Second, a transgenic tobacco split GFP system was designed for in planta detection of the most probable citrus interacting protein partners of P235 and Effector 3. Third, in vitro and in planta studies were performed to show that each of two effectors interacts with and inhibits the functions of multiple citrus proteins belonging to the innate immune pathways. These inhibitory interactions led to a high level of reactive oxygen species (ROS), blocking of bactericidal lipid binding protein (LTP), and induction of premature programmed cell death (PCD), thereby supporting CLas infection and HLB pathogenesis. Finally, an LTP mimic was designed to sequester and block the CLas effector and to rescue the bactericidal activity of LTP.

plant biology↗

bioRxiv2018

Contribution of structural variation to genome structure: TAD fusion discovery and ranking

The significant contribution of structural variants to function, disease, and evolution is widely reported. However, in many cases, the mechanism by which these variants contribute to the phenotype is not well understood. Recent studies reported structural variants that disrupted the three-dimensional genome structure by fusing two topologically associating domains (TADs), such that enhancers from one TAD interacted with genes from the other TAD, and could cause severe developmental disorders. However, no computational method exists for directly scoring and ranking structural variations based on their effect on the three-dimensional structure such as the TAD disruption to guide further studies of their biological function. In this paper, we formally define TAD fusion and provide a combinatorial approach for assigning a score to quantify the level of TAD fusion for each deletion denoted as TAD fusion score. We also show that our method outperforms the approaches which use predicted TADs and overlay the deletion on them to predict TAD fusion. Furthermore, we show that deletions that cause TAD fusion are rare and under negative selection in general population. Finally, we show that our method correctly gives higher scores to deletions reported to cause various disorders (developmental disorder and cancer) in comparison to the deletions reported in the 1000 genomes project.

bioinformatics↗

bioRxiv2017

Ultra-Accurate Complex Disorder Prediction: Case Study Of Neurodevelopmental Disorders

Early prediction of complex disorders (e.g., autism and other neurodevelopmental disorders) is one of the fundamental goals of precision medicine and personalized genomics. An early prediction of complex disorders can have a significant impact on increasing the effectiveness of interventions and treatments in improving the prognosis and, in many cases, enhancing the quality of life in the affected patients. Considering the genetic heritability of neurodevelopmental disorders, we are proposing a novel framework for utilizing rare coding variation for early prediction of these disorders in subset of affected samples. We provide a novel formulation for the Ultra-Accurate Disorder Prediction (UADP) problem and develop a combinatorial framework for solving this problem. The primary goal of this framework, denoted as Odin (Oracle for DIsorder predictioN), is to make prediction for a subset of affected cases while having very low false positive rate prediction for unaffected samples. Note that in the Odin framework we will take advantage of the available functional information (e.g., pairwise coexpression of genes during brain development) to increase the prediction power beyond genes with recurrent variants. Application of our method accurately recovers an additional 8% of autism cases without a sever variant in a known recurrent mutated genes with a less than 1% false positive rate. Furthermore, Odin predicted a set of 391 genes that severe variants in these genes can cause autism or other developmental delay disorders. Odin is publicly available at https://github.com/HormozdiariLab/Odin{dagger}

bioinformatics↗