Biology subjects

Tran, D.

Publications and source records attributed to Tran, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Convergent Inhibitory Cortical Circuit Disruption Drives Genetically Distinct Absence Seizures

Childhood absence epilepsy is one of the most common pediatric epilepsies, characterized by brief involuntary lapse in consciousness and generalized spike-wave discharges (SWDs) on EEG. Despite a growing list of causative genes, the core cortical circuit abnormalities driving this highly stereotyped SWD phenotype remain elusive. Using two well-established absence epilepsy mouse models carrying point mutations in distinct genes altering pre and postsynaptic transmission, stargazer (Cacng2) and tottering (Cacna1a), we show that a specific translaminar inhibitory microcircuit defined by layer 6 corticothalamic neurons (L6 CT) and a novel Tac1+ Pvalb interneuron subtype is disrupted in both models. This early functional defect was followed by a secondary, marked dysfunction of deep-layer somatostatin-expressing (Sst) interneurons that coincides with the postnatal developmental onset of seizures. Crucially, we established the serial causality of these cascading defects by demonstrating that chemogenetic disruption of the L6 CT-Tac1+ Pvalb microcircuit alone in wild-type mice is sufficient to induce both the secondary Sst interneuron dysfunction and contemporaneous emergence of SWDs. Together, these findings reveal a sequential translaminar synaptic dysfunction or domino effect wherein a primary cell-autonomous defect triggers broader circuit adaptations permitting spike-wave hypersynchrony. Our results thus identify a convergent, causative cortical circuit pathology across two genetically heterogeneous absence epilepsy models, highlighting a common functional target for intervention

neuroscience↗

bioRxiv2026

Cutaneous inflammation accelerates the premalignant expansion of melanocytes bearing oncogenic mutations

How the cutaneous microenvironment influences early melanomagenesis is poorly understood. Here, we assessed the effects of three immune perturbations on premalignant melanocyte expansion in an autochthonous mouse model of disease. Depletion of regulatory T (Treg) cells markedly accelerated melanoproliferation, an unexpected phenotype that was associated with monocyte and macrophage infiltration, the production of inflammatory and angiogenic factors, and vascular leakage. In line with these observations, single cell transcriptomic analysis of Treg cell deficient skin revealed robust accumulation of monocyte-derived macrophages with tissue remodeling characteristics. Acute UV irradiation and 2,4-dinitrofluorobenzene (DNFB)-induced contact hypersensitivity had analogous effects on both the cellular microenvironment of the skin and the expansion of local premalignant melanocytes. Treatment with the anti-inflammatory agent dexamethasone attenuated DNFB-induced melanocyte expansion and vascular remodeling. Collectively, these results identify a conserved inflammatory axis linked to the early outgrowth of oncogenic melanocytes in the skin.

cancer biology↗

bioRxiv2026

AlphaFold Database expands to proteome-scale quaternary structures

Protein function is governed by molecular interactions, yet structural coverage of these interactions remains sparse. The AlphaFold Protein Structure Database (AFDB) transformed access to accurate monomeric protein structures at scale. Here, we expand the AFDB to quaternary structures by predicting 31M candidate homo- and heterodimeric protein complexes, compiled from 4,777 proteomes, including model- and global health organisms. We established confidence criteria via analysis of experimentally determined structures, resulting in 1.81M high-confidence predictions. These models enabled the discovery of emergent structures and topologies not present in monomeric predictions. Additionally, the top 1% of structural clusters accounted for [~]44% of all complexes, and [~]8.3% of clusters were conserved across multiple domains of life, pointing to a substantial fraction of ancient, universally retained assemblies. Structural search highlighted that high-confidence predictions are anchored in experimental multimer space, yet 31.3% extend beyond detectable PDB coverage. These freely accessible proteome-scale predictions facilitate functional and mechanistic hypothesis generation across biology.

synthetic biology↗

bioRxiv2026

Recapitulating whipworm development in vitro using caecaloids

Whipworms (Trichuris spp.) are intracellular intestinal parasites that develop within the host caecal epithelium, yet the host signals that regulate their growth and developmental progression remain poorly understood. Progress in studying these processes has been limited by the lack of physiologically relevant in vitro systems capable of supporting sustained whipworm development. Here, we established an in vitro infection system using caecal organoids (caecaloids) and evaluated their capacity to support sustained growth and morphological development of Trichuris muris larvae. To rigorously validate this system, we generated a comprehensive and up-to-date anatomical and biometrical reference dataset describing the whole-body growth and tissue-level morphogenesis of T. muris throughout its life cycle in vivo. Quantitative analysis across larval and adult stages confirmed that the trajectory of parasite growth is largely conserved across host mouse strains and provided a detailed contextualised description of the development of key anatomical structures of T. muris. Using this reference framework, we evaluated parasite growth and development in long-term T. muris-caecaloid co-cultures. Larvae invading the caecaloid epithelium remained intracellular within syncytial tunnels and exhibited sustained growth over extended culture periods. in vitro parasites developed increasing anatomical complexity, including formation of the bacillary band, stichosome, intestine, and rectum. Importantly, quantitative comparisons revealed that larvae developing within caecaloids follow growth trajectories and morphological developmental patterns closely resembling those observed in vivo. This study therefore presents the first detailed anatomical and morphometric framework for validating whipworm development in an organoid system and provides concrete evidence that the caecaloid epithelium is sufficient to trigger and sustain whipworm growth and morphogenesis, establishing caecaloids as a powerful experimental platform for investigating Trichuris infection and development.

microbiology↗

bioRxiv2025

Single-Cell Multiomic Profiling Uncovers Radiation Dosage-Sensitive, Cluster-Specific Regulatory Dynamics in Glioblastoma

Glioblastoma (GBM) is an aggressive brain tumor that inevitably recurs after chemoradiotherapy, resulting in poor patient outcomes. Given GBMs cellular heterogeneity, we hypothesized that radiation induces sub-population specific alterations to survive and adapt to radiation stress. We performed integrated single-cell RNA-seq and ATAC-seq analyses in Glioma Stem-Like Cultures three hours after they were exposed to clinically relevant radiation doses. Radiation reshaped the cellular landscape, altering both cell type composition and GBM subtype distribution. Cluster-specific and shared transcriptional programs were induced in a dose-dependent manner, with differentially expressed genes enriching distinct biological pathways. Chromatin accessibility analyses revealed parallel cluster-specific remodeling, with both opening and closing of regulatory elements linked to functional pathway shifts. Notably, 2 Gy and 6 Gy exposures elicited conserved transcriptional profiles in RNA clusters across different radiation doses. Together, these results highlight immediate radiation-induced transcriptional and chromatin remodeling programs in GBM at single-cell resolution and identify conserved cluster-specific adaptations that may underlie therapeutic resistance.

cancer biology↗

bioRxiv2025

Dynamic Stiffening to Improve Vasculogenesis of hiPSC-Derived Endothelial Progenitors

Multiple groups have reported on the impact of hydrogel stiffness on vascular network formation in vitro, with overall findings indicating that less stiff hydrogels better support vasculogenesis. However, the majority of this research utilized hydrogels with static stiffness, even though vasculogenesis occurs in tandem with changes in extracellular matrix material properties. To that end, we hypothesize that dynamic modulation of hydrogel stiffness during the process of vasculogenesis, recapitulating changes observed during embryonic development, would improve vascular network formation. Using our Collagen I/Norbornene-modified hyaluronic acid hydrogel system, we swelled in additional crosslinker and photoinitiator and exposed the hydrogel to UV light, enabling hydrogel stiffening at user-defined time points with no significant effect on cell viability. We observed that in situ stiffening at early time points, prior to the onset of significant cell migration, resulted in more robust vascular network formation relative to unstiffened controls, while stiffening at later time points disrupted existing vascular networks. These trends continued in in vivo experiments in nude mice, with cell-laden hydrogels stiffened at early time points resulting in improved blood flow, while those stiffened at later time points had the opposite effect. We hypothesized that this was due to differential impacts of focal adhesion kinase (FAK) activation following in situ stiffening, as supplementation with a Rho kinase inhibitor, downstream of FAK, partially reversed the effects of in situ stiffening. Taken together, this research demonstrates the benefits of incorporating dynamic cues into hydrogel design to create more physiologically relevant vasculature.

bioengineering↗

bioRxiv2025

A blueprint for mutation-defined hallmark vulnerabilities across human cancers

Hallmark gene mutations shape cancer cell vulnerabilities and inform drug discovery1-3. A systematic map of hallmark gene mutation-defined cancer dependencies and therapeutic responses is essential to uncover novel targets and refine therapeutic strategies. Here, we present the first pan-cancer blueprint of hallmark vulnerabilities, systematically linking hallmark gene mutation markers to cancer cell dependencies and drug sensitivities across 22 cancer cohorts. We integrated multi-omics data from patient tumours with large-scale CRISPR-Cas9 screens and pharmacologic profiling of over a thousand cancer cell lines. Our analysis revealed the cancer type-specific nature of hallmark gene expression programs, uncovered previously unrecognised mutation-target gene dependencies, and highlighted metabolic programs as a dominant class of functional vulnerabilities. Notably, we identified oxidative phosphorylation (OXPHOS) addiction in CDKN2A-loss lung squamous cell carcinoma (LUSC) and experimentally validated this dependency. Our validation highlights the greater selectivity of CDKN2A-loss LUSC cells to metformin, an FDA-approved antidiabetic drug known for its OXPHOS inhibitory activity. Proteogenomic integration further prioritised targets overexpressed in mutant tumours, constituting therapeutic windows. Pharmacologic profiling identified both oncology and non-oncology agents with selective activity in mutation-defined subgroups, revealing opportunities for drug repurposing. Our machine learning framework, Comet-X, for the first time fully leveraged gene mutation combinations to predict these target dependencies and drug responses. The resulting pan-cancer mutation-dependency map provides a comprehensive resource of hallmark gene targets and candidate therapeutics, stratified by mutation markers, to pave the way for drug development, clinical trial design and discovery research.

cancer biology↗

bioRxiv2025

A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress

A hallmark of heart disease is gene dysregulation and reactivation of fetal gene programs. Reactivation of these fetal programs has compensatory effects during heart failure, depending on the type and stage of the underlying cardiomyopathy. Thousands of putative cardiac gene regulatory elements have been identified that may control these programs, but their functions are largely unknown. We profile genome-wide changes to gene expression and chromatin structure in cardiomyocytes derived from human pluripotent stem cells. We identify and characterize a gene regulatory element essential for the regulation of MYH6, which encodes human fetal myosin. Using chromatin conformation assays in combination with epigenome editing, we find that gene regulation is mediated by direct interaction between MYH6 and the enhancer. We also find that enhancer activation alters cardiomyocyte response to the hypertrophy-inducing peptide endothelin-1. Enhancer activation prevents polyploidization and changes in calcium dynamics following stress with endothelin-1. Collectively, these results identify regulatory mechanisms of cardiac gene expression programs that modulate cardiomyocyte maturation, cellular stress response, and could serve as potential therapeutic targets.

genomics↗

bioRxiv2025

CytoAnalyst: A web-based platform for comprehensive single-cell RNA sequencing analysis

Single-cell technologies have revolutionized our ability to study cellular heterogeneity and dynamics at unprecedented resolutions. In this fast-growing field, it becomes increasingly challenging to navigate the vast amount of tools and steps for analysis. It is particularly difficult to integrate and analyze large datasets that require extensive collaborations and customized pipelines to obtain robust results. We present CytoAnalyst, a web-based platform that offers a number of important advantages over existing tools for single-cell analysis. First, the platform enables custom pipeline configuration using an efficient study management system and a broad range of analysis modules. Second, the platform supports parallel analysis instances, facilitating the comprehensive comparison of different methods or parameter settings available at each analysis step. Third, the advanced sharing system facilitates real-time synchronization among team members and seamless analysis continuation across different devices. Finally, the multi-grid visualization system supports simultaneous display of different data aspects, allowing for the comparison of multiple labels and plots side-by-side for comprehensive data insights, with the ability to save and reload visualization settings at any analysis step. The platform incorporates multiple blending modes, allowing users to combine plots in various ways for comprehensive data exploration. CytoAnalyst supports a high level of analytical rigor while providing user-friendly and flexible operations through its carefully designed interface and extensive documentation. The platform supports all major web browsers and is freely available at https://cytoanalyst.tinnguyen-lab.com.

bioinformatics↗

bioRxiv2025

Discovery of a VHL molecular glue degrader of GEMIN3 by Picowell RNA-seq

Targeted protein degradation (TPD) is an emerging therapeutic modality in which small molecules are used to recruit targets to the natural protein degradation machinery of the cell. Molecular glue degraders (MGD) are monovalent small molecules that accomplish this by redirecting E3 ubiquitin ligases to target proteins, offering the potential to degrade previously unliganded and "undruggable" proteins in cancer, neurodegenerative, and other diseases. While attractive due to their drug-like properties, MGDs are exceptionally hard to discover and have largely been identified serendipitously. The Von Hippel-Lindau (VHL) E3 ligase is the second most widely used effector for TPD, though current VHL-based degraders are primarily large heterobifunctional PROTACs (proteolysis-targeting chimeras) designed using target-based ligands. Here, we have instead pursued target-agnostic discovery of VHL MGDs leveraging proprietary ultra-miniaturized microfluidics devices (Picowells) to facilitate unbiased RNA-seq screening of a biased E3-focused library. This resulted in dGEM3, a novel VHL molecular glue that targets the survival of motor neuron (SMN) complex member GEMIN3 for degradation. Through a combination of cellular, biochemical, and biophysical assays, we have characterized the GEMIN3 degron within its helicase ATP-binding domain, and how the kinetics of ternary complex formation impact degradation. These findings provide insights on the re-programmability of VHL for novel targets using drug-like molecular glues.

biochemistry↗

bioRxiv2024

FAK activity exacerbates disturbed flow-mediated atherosclerosis via VEGFR2-Cbl-NF-κB signaling.

Atherosclerosis develops at predictable sites in the vasculature where branch points and curvatures create non-laminar disturbed flow. This disturbed flow causes vascular inflammation by increased endothelial cell (EC) barrier permeability and the expression of inflammatory genes such as vascular cell adhesion molecule-1 (VCAM-1). Vascular endothelial growth factor receptor 2 (VEGFR2) is important for flow-induced EC inflammation; however, there are still some gaps in the signaling pathway. Focal adhesion kinase (FAK) is a protein tyrosine kinase whose expression has been implicated in flow-mediated signaling in ECs. However, the link between FAK and VEGFR2 in flow-mediated inflammation signaling has remained unelucidated. Here we found that priming of VEGFR2 with VEGF was critical for flow-mediated activation of FAK and NF-kB. Mechanistically, FAK activation triggers tyrosine phosphorylation of Casitas B-lineage lymphoma (CBL; an E3 ubiquitin ligase) that interacts with VEGFR2 under flow conditions. Further, Apoe-/- mice fed a western diet (WD) exhibited increased FAK activity within the atheroprone disturbed flow region of the inner aortic arch compared to the outer arch. Disturbed flow-induced FAK activation is associated with elevated VEGFR2 on the surface of ECs of the inner aortic arch, but not in the outer arch. Taken together, these data suggest that suppression of augmented FAK activity under disturbed flow may prove beneficial in reducing pro-inflammatory signaling of the endothelial layer.

cell biology↗

bioRxiv2024

Developmental disruption of Mef2c in Medial Ganglionic Eminence-derived cortical inhibitory interneurons impairs cellular and circuit function

MEF2C is strongly linked to various neurodevelopmental disorders (NDDs) including autism, intellectual disability, schizophrenia, and attention-deficit/hyperactivity. Mice constitutively lacking one copy of Mef2c, or selectively lacking both copies of Mef2c in cortical excitatory neurons, display a variety of behavioral phenotypes associated with NDDs. The MEF2C protein is a transcription factor necessary for cellular development and synaptic modulation of excitatory neurons. MEF2C is also expressed in a subset of cortical GABAergic inhibitory neurons, but its function in those cell types remains largely unknown. Using conditional deletions of the Mef2c gene in mice, we investigated the role of MEF2C in Parvalbumin-expressing Interneurons (PV-INs), the largest subpopulation of cortical GABAergic cells, at two developmental timepoints. We performed slice electrophysiology, in vivo recordings, and behavior assays to test how embryonic and late postnatal loss of MEF2C from GABAergic interneurons impacts their survival and maturation, and alters brain function and behavior. We found that loss of MEF2C from PV-INs during embryonic, but not late postnatal, development resulted in reduced PV-IN number and failure of PV-INs to molecularly and synaptically mature. In association with these deficits, early loss of MEF2C in GABAergic interneurons lead to abnormal cortical network activity, hyperactive and stereotypic behavior, and impaired cognitive and social behavior. Our findings indicate that MEF2C expression is critical for the development of cortical GABAergic interneurons, particularly PV-INs. Embryonic loss of function of MEF2C mediates dysfunction of GABAergic interneurons, leading to altered in vivo patterns of cortical activity and behavioral phenotypes associated with neurodevelopmental disorders.

neuroscience↗

bioRxiv2024

Multimodal classification of neurons in the lateral septum

The lateral septum (LS) is a ventral forebrain nucleus that modulates complex social and affective behaviors. These behaviors emerge from heterogeneous neuronal populations whose molecular identity and developmental origins remain poorly defined. We profiled the transcriptional identity of mature LS neurons derived from two progenitor lineages distinguished by their embryonic origin and Nkx2.1 expression history, identifying 22 molecularly distinct subtypes. Nkx2.1-lineage neurons are enriched for select cell adhesion and communication molecules; however, subtypes from distinct developmental origins can converge onto similar molecular profiles when residing within the same LS subregion. The graded expression of genes related to synaptic signaling is a primary axis defining the taxonomy of LS neurons. Using transcriptional markers, we labeled non-overlapping neuronal populations and characterized their connectivity, morphology, and electrophysiology. Together, these findings define the extent of LS neuronal diversity and provide a framework for understanding how complex behaviors are regulated by the LS.

neuroscience↗

bioRxiv2023

Spatial and Temporal Coordination of Force-generating Actin-based Modules Drives Membrane Remodeling In Vivo

Membrane remodeling drives a broad spectrum of cellular functions, and it is regulated through mechanical forces exerted on the membrane by cytoplasmic complexes. Here, we investigate how actin filaments dynamically tune their structure to control the active transfer of membranes between cellular compartments with distinct compositions and biophysical properties. Using intravital subcellular microscopy in live rodents we show that: a lattice composed of linear filaments stabilizes the granule membrane after fusion with the plasma membrane; and a network of branched filaments linked to the membranes by Ezrin, a regulator of membrane tension, initiates and drives to completion the integration step. Our results highlight how the actin cytoskeleton tunes its structure to adapt to dynamic changes in the biophysical properties of membranes.

cell biology↗

bioRxiv2023

Shifts in attention drive context-dependent subspace encoding in anterior cingulate cortex during decision making

Attention is a cognitive faculty that selects part of a larger set of percepts, driven by cues such as stimulus saliency, internal goals or priors. The enhancement of the attended representation and inhibition of distractors have been proposed as potential neural mechanisms driving this selection process. Yet, how attention operates when the cue has to be internally constructed from conflicting stimuli, decision rules, and reward contingencies, is less understood. Here we recorded from populations of neurons in the anterior cingulate cortex (ACC), an area implicated in ongoing error monitoring and correction during decision conflicts, in a challenging attention-shifting task. In this task, mice had to attend to the rewarded modality when presented identical auditory and visual stimuli in two contexts without direct external cues. In the ACC, the irrelevant stimulus continuously became less decodable than the relevant stimulus as the trial progressed to the decision point. This contrasted strongly with our previous findings in V1 where both relevant and irrelevant stimuli were equally decodable throughout the trial. Using analytical tools and a recurrent neural network (RNN) model, we found that the linearly independent representation of stimulus modalities in ACC was well suited to context-gated suppression of a stimulus modality. We demonstrated that the feedback structure of lateral connections in the RNN consisted of excitatory interactions between cell ensembles representing the same modality and mutual inhibition between cell ensembles representing distinct stimulus modalities. Using this RNN model showing signatures of context-gated suppression, we predicted that the level of contextual modulation of individual neurons should be correlated with their relative responsiveness to the two stimulus modalities used in the task. We verified this prediction in recordings from ACC neurons but not from recordings from V1 neurons. Therefore, ACC effectively operates on low-dimensional neuronal subspaces to combine stimulus related information with internal cues to drive actions under conflict.

neuroscience↗

bioRxiv2023

Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection

Congenital cytomegalovirus (cCMV) is the leading infectious cause of neurologic defects in newborns with particularly severe sequelae in the setting of primary CMV infection in the first trimester of pregnancy. The majority of cCMV cases worldwide occur after non-primary infection in CMV-seropositive women; yet the extent to which pre-existing natural CMV-specific immunity protects against CMV reinfection or reactivation during pregnancy remains ill-defined. We previously reported on a novel nonhuman primate model of cCMV in rhesus macaques where 100% placental transmission and 83% fetal loss were seen in CD4+ T lymphocyte-depleted rhesus CMV (RhCMV)-seronegative dams after primary RhCMV infection. To investigate the protective effect of preconception maternal immunity, we performed reinfection studies in CD4+ T lymphocyte-depleted RhCMV-seropositive dams inoculated in late first / early second trimester gestation with RhCMV strains 180.92 (n=2), or RhCMV UCD52 and FL-RhCMV{Delta}Rh13.1/SIVgag, a wild-type-like RhCMV clone with SIVgag inserted as an immunological marker (n=3). An early transient increase in circulating monocytes followed by boosting of the pre-existing RhCMV-specific CD8+ T lymphocyte and antibody response was observed in the reinfected dams but not in control CD4+ T lymphocyte-depleted dams. Emergence of SIV Gag-specific CD8+ T lymphocyte responses in macaques inoculated with the FL-RhCMV{Delta}Rh13.1/SIVgag virus confirmed reinfection. Placental transmission was detected in only one of five reinfected dams and there were no adverse fetal sequelae. Viral whole genome, short-read, deep sequencing analysis confirmed transmission of both reinfection RhCMV strains across the placenta with [~]30% corresponding to FL-RhCMV{Delta}Rh13.1/SIVgag and [~]70% to RhCMV UCD52, consistent with the mixed human CMV infections reported in infants with cCMV. Our data showing reduced placental transmission and absence of fetal loss after non-primary as opposed to primary infection in CD4+ T lymphocyte-depleted dams indicates that preconception maternal CMV-specific CD8+ T lymphocyte and/or humoral immunity can protect against cCMV infection. Author SummaryGlobally, pregnancies in CMV-seropositive women account for the majority of cases of congenital CMV infection but the immune responses needed for protection against placental transmission in mothers with non-primary infection remains unknown. Recently, we developed a nonhuman primate model of primary rhesus CMV (RhCMV) infection in which placental transmission and fetal loss occurred in RhCMV-seronegative CD4+ T lymphocyte-depleted macaques. By conducting similar studies in RhCMV-seropositive dams, we demonstrated the protective effect of pre-existing natural CMV-specific CD8+ T lymphocytes and humoral immunity against congenital CMV after reinfection. A 5-fold reduction in congenital transmission and complete protection against fetal loss was observed in dams with pre-existing immunity compared to primary CMV in this model. Our study is the first formal demonstration in a relevant model of human congenital CMV that natural pre-existing CMV-specific maternal immunity can limit congenital CMV transmission and its sequelae. The nonhuman primate model of non-primary congenital CMV will be especially relevant to studying immune requirements of a maternal vaccine for women in high CMV seroprevalence areas at risk of repeated CMV reinfections during pregnancy.

immunology↗

bioRxiv2022

SARS-CoV-2 Envelope-mediated Golgi pH dysregulation interferes with ERAAP retention in cells

Endoplasmic reticulum (ER) aminopeptidase associated with antigen processing (ERAAP) trims peptide precursors in the ER for presentation by major histocompatibility (MHC)-I molecules to surveying CD8+ T-cells. This function allows ERAAP to regulate the nature and quality of the peptide repertoire and, accordingly, the resulting immune responses. We recently showed that infection with murine cytomegalovirus leads to a dramatic loss of ERAAP levels in infected cells. In mice, this loss is associated with the activation of QFL T-cells, a subset of T-cells that monitor ERAAP integrity and eliminate cells experiencing ERAAP dysfunction. In this study, we aimed to identify host factors that regulate ERAAP expression level and determine whether these could be manipulated during viral infections. We performed a CRISPR knockout screen and identified ERp44 as a factor promoting ERAAP retention in the ER. ERp44s interaction with ERAAP is dependent on the pH gradient between the ER and Golgi. We hypothesized that viruses that disrupt the pH of the secretory pathway interfere with ERAAP retention. Here, we demonstrate that expression of the Envelope (E) protein from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) leads to Golgi pH neutralization and consequently decrease of ERAAP intracellular levels. Furthermore, SARS-CoV-2-induced ERAAP loss correlates with its release into the extracellular environment. ERAAPs reliance on ERp44 and a functioning ER/Golgi pH gradient for proper localization and function led us to propose that ERAAP serves as a sensor of disturbances in the secretory pathway during infection and disease.

cell biology↗

bioRxiv2022

Inflammatory cytokines rewire the proinsulin interaction network in human islets

Aberrant biosynthesis and secretion of the insulin precursor proinsulin occurs in both Type I and Type II diabetes (T1D, T2D). Inflammatory cytokines are implicated in pancreatic islet stress in both forms of diabetes but the mechanisms remain unclear. Here we examined how the diabetes associated cytokines interleukin-1{beta} and interferon-{gamma} alter proinsulin interactions with proteins that regulate its folding, trafficking, and secretion. Human islets treated with cytokines exhibited secretion of proinsulin, IL6 and nitrite, as well as evidence of endoplasmic reticulum (ER) stress. Unbiased proinsulin Affinity Purification-Mass Spectrometry revealed a proinsulin interactome reshaped by cytokines relative to controls. Cytokine treatment increased proinsulin binding to multiple ER chaperones and oxidoreductases, including the major ER chaperone BiP. Moreover, increased BiP binding was an adaptive response required to maintain proinsulin folding in the inflammatory environment. Cytokines also regulated novel interactions between proinsulin and T1D and T2D GWAS candidate proteins not previously known to interact with proinsulin (e.g., Ataxin-2) and these GWAS proteins formed a tight network with each other. Finally, cytokines induced proinsulin interactions with a cluster of microtubule motor proteins. Consistent with a role for these proteins in proinsulin trafficking and release, chemical destabilization of microtubules with Nocodazole exacerbated cytokine induced proinsulin secretion. Together, the data quantitatively map the proinsulin interactome rewired by cytokines, shedding new light on how human proinsulin biosynthesis is dysregulated by an inflammatory environment.

cell biology↗