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Sun, J.

Publications and source records attributed to Sun, J..

At least 127 records · Page 7Linked to original sources

Mechanisms of KCNQ1 gating modulation by KCNE1/3 for cell-specific function

KCNQ1 potassium channels are essential for physiological processes such as cardiac rhythm and intestinal chloride secretion. KCNE-family subunits (KCNE1-5) associate with KCNQ1, conferring distinct properties across various tissues. KCNQ1 activation requires membrane depolarization and phosphatidylinositol 4,5-bisphosphate (PIP2) whose cellular levels are controlled by Gq-coupled GPCR activation. While modulation of KCNQ1s voltage-dependent activation by KCNE1/3 is well-characterized, their effects on PIP2-dependent gating of KCNQ1 via GPCR signaling remain less understood. Here we resolved structures of KCNQ1-KCNE1 and reassessed reported KCNQ1-KCNE3 structures with and without PIP2. We revealed that KCNQ1-KCNE1/3 complexes feature two PIP2-binding sites, with KCNE1/3 contributing to a previously overlooked, uncharacterized site involving residues critical for voltage sensor and pore domain coupling. Via this site, KCNE1 and KCNE3 distinctly modulate the PIP2-dependent gating, in addition to the voltage sensitivity, of KCNQ1. Consequently, KCNE3 converts KCNQ1 into a voltage-insensitive PIP2-gated channel governed by GPCR signaling to maintain ion homeostasis in non-excitable cells. KCNE1, by significantly enhancing KCNQ1s PIP2 affinity and resistance to GPCR regulation, forms predominantly voltage-gated channels with KCNQ1 for conducting the slow-delayed rectifier current in excitable cardiac cells. Our study highlights how KCNE1/3 modulates KCNQ1 gating in different cellular contexts, providing insights for tissue-specifically targeting multi-functional channels.

biochemistry↗

Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient mice.

CHD8 mutations cause autism spectrum disorder, cognitive deficits, and macrocephaly. Chd8+/- mouse models exhibit macrocephaly and transcriptional pathology, with inconsistent findings regarding neurogenesis, neuron function, and behavior. Via stereology and single nucleus transcriptomics (snRNA-seq), we found increased Chd8+/- cortical volume was not explained by increase in neuron number. Differential expression (DE) was present across cortical cell types, with excitatory neurons exhibiting high DE burden and shared and subclass-specific DE signatures. Bulk RNA-seq DE of constitutive Chd8+/- and conditional Camk2a-Cre Chd8+/-mice identified shared transcriptional pathology. DE in synaptosomal versus nuclear mRNA identified overlapping DEGs, but also significant differences and exaggerated synaptosomal changes. Building on DE findings implicating glutamatergic neurons, we found Chd8+/-mice exhibited altered excitatory neuron spine density and dynamics, decreased GCaMP activity correlation, and sleep perturbation. Thus, Chd8 haploinsufficiency causes lasting excitatory neuron dysfunction, perturbs RNA regulation beyond transcription, and impacts neuronal properties, cortical microcircuits, and behavior.

genomics↗

A Cell Type-Specific Role for Tubb6 in Ciliogenesis of Xenopus Epidermal Multiciliated Cells

Cilia are microtubule-based organelles found on the surface of most eukaryotic cells. These microtubules are composed of - and {beta}-tubulin heterodimers, and different tubulin isotypes can confer distinct properties to microtubules. Despite their importance, the contribution of individual tubulin isotype to cilia formation and function remains largely unexplored in vertebrates. Here, we identify a critical role for the {beta}-tubulin isotype Tubb6 in the formation of motile cilia in Xenopus epidermal multiciliated cells (MCCs). Tubb6 mRNA is selectively expressed in MCCs, and its protein product localizes to ciliary axonemes. Loss of Tubb6 leads to a marked reduction in cilia number and length, resulting in defective MCC function. In contrast, mono-motile cilia in the gastrocoel roof plate are unaffected by Tubb6 depletion, suggesting a selective requirement for ciliogenesis in MCCs. Together, our findings uncover a cell type-specific role for Tubb6 in motile cilia formation and highlight the functional specialization of tubulin isotypes in vertebrate cilia assembly.

developmental biology↗

In-cell Proteomics Enables High-Resolution Spatial and Temporal Mapping of Early Xenopus tropicalis Embryos

Early embryonic development requires tightly regulated molecular programs to coordinate cell division, fate specification, and spatial patterning. While transcriptomic profiling is widely performed, proteomic analyses of early vertebrate embryos remain limited due to technical challenges in embryonic sample preparation. Here, we propose an "in-cell proteomics" approach, which bypasses cell lysis and yolk depletion, processes individual embryos directly in functionalized filter devices, and generates liquid chromatography-mass spectrometry (LC-MS)-friendly samples in an extremely robust and streamlined manner. Combined with a single-shot data-independent acquisition (DIA) MS workflow, this approach enabled us to consistently quantify [~]6,200 proteins from a single Xenopus tropicalis embryo, representing the deepest proteomic coverage of early X. tropicalis development reported to date. Investigation of the temporal proteomes across five cleavage stages (1- to 16-cell) revealed a drastic proteomic shift between 2- and 4-cell stages, followed by more gradual transitions thereafter. Spatial analysis of dissected 8-cell blastomeres uncovered pronounced molecular asymmetry along the animal-vegetal axis, while dorsal-ventral differences were minimal. This study establishes a novel in-cell proteomics technology in conjunction with DIA-MS as a robust platform for high-resolution, low-input developmental proteomics analysis, and provides a comprehensive spatiotemporal protein atlas for early X. tropicalis embryos.

biochemistry↗

Endothelial c-IAP2 Loss Amplifies P2X7 Receptor-Driven Inflammation and Worsens Infection-Associated Pulmonary Hypertension

Schistosomiasis-associated Pulmonary Hypertension (Sch-PH) is the most common form of group I PH worldwide. Recently, data revealed that the preclinical animal model of Sch-PH exhibited gut and lung microbiome dysbiosis linked to significant endothelial dysfunction and microvascular apoptosis, but the role of pro/anti-apoptosis sensors, such as the inhibitor of apoptosis protein 2 (c-IAP2) and purinergic receptor P2X7 (P2X7R), remained unclear. Using a novel Cdh5cre-ERT2;cIAP1-/-;cIAP2fl/fl animal model, this study investigated the contribution of endothelial c-IAP2 in this process, revealing P2X7R overexpression as a putative target in the onset of Sch-PH. Pharmacologically, inhibition of P2X7R function confirmed its role in promoting lung endothelial death and disease progression. Moreover, data suggest that microbiome-associated metabolic alterations in Sch-PH seem linked to microvascular endothelial apoptosis driven by ATP/P2X7R overactivation and suppressed c-IAP2 expression. Indeed, genetic ablation of endothelial c-IAP2 expression was sufficient to induce PH-like features in mice, with echocardiography indicating a higher pulmonary acceleration time (PAT), PAT/pulmonary ejection time (PET), and right ventricular free wall thickness after IP/IV-Egg challenge compared to controls. These findings suggest a significant contribution of lung endothelial P2X7R activation and c-IAP2 suppression to Sch-PH pathology, highlighting them as promising novel therapeutic targets for this life-threatening illness.

pharmacology and toxicology↗

IL-17A-driven Macrophage Disorder Promotes Plaque Instability in Psoriatic Atherosclerosis

Psoriasis is a common chronic inflammatory skin disease that predisposes individuals to cardiovascular diseases such as atherosclerosis. However, the underlying mechanisms linking these conditions have not yet been fully elucidated. Recent studies have indicated that the inflammatory cytokine IL-17A plays a significant role in both diseases. The aim of this study was to investigate how psoriasis affects the stability of atherosclerotic plaques via the IL-17A/IL-17RA pathway. We performed single-cell sequencing on patients with both psoriasis and atherosclerosis to analyze changes in the immune microenvironment within their carotid plaques and psoriatic lesions. We found that IL-17A significantly upregulated the expression of pro-inflammatory factors (e.g., CXCL8) in macrophages of psoriatic atherosclerosis patients, leading to weakening of the fibrous cap structure of plaques. Additionally, IL-17A further exacerbated plaque instability by interfering with macrophage lipid metabolism, particularly sphingolipid metabolism. Finally, using in vitro experiments and animal models, we demonstrated that IL-17A enhances pro-inflammatory and metabolic abnormalities in macrophages by downregulating PPAR{gamma}. Therapeutic strategies targeting IL-17A may contribute to the simultaneous mitigation of psoriasis and atherosclerosis-associated cardiovascular risk, providing new directions for clinical intervention.

cell biology↗

TWIST1 drives endothelial-to-mesenchymal-transition to stabilize atherosclerotic plaques

Atherosclerosis progresses from fatty streaks to complex plaques, with rupture leading to life-threatening complications. Endothelial-to-mesenchymal transition (EndMT) is associated with advanced atherosclerotic plaques, but its role in plaque progression remains unclear. To investigate this, we analyzed the role of TWIST1, a key EndMT-driving transcription factor, in plaque development. Using single-cell RNA sequencing of atherosclerotic plaques from hypercholesterolemic mice with inducible deletion of Twist1 from endothelial cells (Twist1ECKO ApoE-/-) we demonstrate that Twist1 regulates endothelial cell heterogeneity by promoting cell states expressing EndMT markers. Cell tracking confirmed that Twist1 induces EndMT in advanced plaques. Mechanistically, we found that TWIST1 contributes to EndMT by promoting endothelial migration and proliferation through the transcriptional coactivator PELP1. Additionally, TWIST1 induces AEBP1 transcription, which upregulates COL4A1 to drive endothelial proliferation. Analyses of murine brachiocephalic plaques show that endothelial Twist1 promotes plaque growth, collagen deposition, and ACTA2-positive cell accumulation, hallmarks of plaque stability, while reducing necrosis and macrophage infiltration, features of plaque instability. Moreover, TWIST1 expression was associated with asymptomatic human carotid atherosclerosis and predicts favourable clinical outcomes. These findings challenge the prevailing view that EndMT destabilizes plaques, by suggesting that TWIST1-driven EndMT can promote plaque stability, offering new insights into atherosclerosis pathophysiology and therapeutic potential.

pathology↗

CNVPipe: An enhanced pipeline for accurate analysis of copy number variation from whole-genome sequencing

Copy number variations (CNVs) are critical contributors to the genetic architecture of complex diseases, yet many existing pipelines for whole-genome sequencing (WGS) data exhibit persistently high false discovery rates (FDR). Here, we introduce CNVPipe, an enhanced workflow that integrates widely used CNV-calling tools with a novel machine-learning framework to achieve lower FDR and higher sensitivity. CNVPipe also provides a specialised module for single-cell CNV analysis, featuring a new model that accurately estimates the ploidy of single cells to get integer copy number profile. Benchmark evaluations demonstrate that CNVPipe outperforms current pipelines in various genomic contexts. In addition to detecting recurrent CNVs in paediatric developmental disorders, CNVPipe enables large-scale functional genomics applications involving stem cell technologies. Moreover, its application to sparse single-cell DNA sequencing data provides a new aspect of research in cancer evolution. Collectively, these findings underscore the versatility and reliability of CNVPipe as a comprehensive solution for CNV detection in WGS-based research.

systems biology↗

Beyond the Axoneme: Whole-Cell Proteomics Identifies Novel Regulators of Ciliogenesis in Xenopus Epidermal Multiciliated Cells

Motile cilia generate directional fluid flow critical for development and tissue homeostasis, and their dysfunction underlies a range of human diseases. Prior proteomic studies have focused on isolated axonemes, leaving the regulatory components of ciliogenesis located in other cellular compartments of multiciliated cells (MCCs) largely unidentified. To bridge this gap, we performed whole-cell proteomic profiling of MCCs in Xenopus using an inducible system that enables selective MCC-enrichment. Leveraging a single-vessel in-cell proteomics approach with ultra-high sample preservation, we identified over 9,000 proteins, including 832 upregulated in MCCs. These encompassed both established ciliary components and novel candidates localized to distinct ciliary structures. Functional validation confirmed the involvement of previously uncharacterized proteins in ciliogenesis. This study presents a high-resolution, whole-cell proteome of vertebrate MCCs, providing critical insights into the molecular networks that govern ciliogenesis and offering a valuable resource for understanding the mechanisms of cilia-related disorders.

developmental biology↗

Multiple-omics analyses of the Alviniconcha holobiont reveal multi-faceted adaptations to deep-sea hydrothermal vents

Deep-sea hydrothermal vents are extreme environments with constantly fluctuating physicochemical conditions - but dense animal aggregations thrive primarily through symbiosis with chemoautotrophic bacteria to exploit the unusual chemistry. Alviniconcha snails, which harbor symbionts in their enlarged gill at an intracellular-extracellular intermediate state, are a prime example. Here, we present chromosome-level genomes of two Alviniconcha species (A. adamantis and A. marisindica) to investigate the adaptations of this holobiont. Significant expansion of solute carrier families enhances nutrient transport between the two parties. Alviniconcha lacks complete methionine biosynthesis pathways, compensated by symbiont provisioning, highlighting host-symbiont metabolic complementarity. High myoglobin expression in gills, contradicting prior reports of hemoglobin, suggests myoglobin-mediated oxygen storage to mitigate fluctuating environmental oxygen. Spatial transcriptomics further delineated gills functional zones on the gill filament responsible for symbiont digestion via phagocytosis in bacteriocytes, oxygen transport in secretory zones, and ciliary water flow regulation. Our findings elucidate molecular and physiological adaptations underpinning the Alviniconcha holobionts success in dynamic and treacherous vent ecosystems.

microbiology↗

The identification and characterization of hillocks in the postnatal mouse and human airway

Adult lung regeneration has been deeply scrutinized over the past decade. In contrast, the injury resistance mechanisms of the neonatal and pediatric airway have received considerably less attention despite the manifest clinical importance. We recently reported the discovery of the airway hillock in adult murine and human airways. Adult hillocks are stratified structures with luminal squamous barrier cells overlying a dedicated basal stem cell population. Functionally, hillocks serve as an injury-resistant reservoir of dedicated hillock stem cells that can resurface and repopulate the airway epithelium after severe damage. Indeed, hillock basal stem cells undergo massive clonal expansion in the process of repopulating denuded airway epithelium. Since the postnatal lung encounters injuries that can result in airway epithelial denudation in the setting of respiratory infection or aspiration, we sought to assess whether hillocks are present in the neonatal airway. In this manuscript we identify and characterize hillocks in postnatal mouse and human pediatric airways. We show that hillocks are present in mice from postnatal day 3 onwards and that they expand in size through adulthood. The earliest hillocks are functionally immature, but they acquire their injury resistance properties over the course of postnatal maturation. By re-analyzing published pediatric scRNAseq data, we identify cells with a hillock squamous cell gene signature that is conserved across species. Finally, we identify bona fide hillocks in an 8-month-old infant and an 8-year-old child. We now wonder whether the presence and maturation of hillocks has implications for disorders of the neonatal and childhood airway. More specifically, we hypothesize that the incomplete maturation of hillocks could create a window of vulnerability in neonates who may be particularly susceptible to airway damage in the setting of infection or aspiration. Thus, there is a need to define when human hillocks first form and establish the time window during which they functionally mature as a prelude to determining whether the appearance and properties of hillocks correlate to clinical phenotypes and outcomes.

developmental biology↗

DILP8 serves as a mature follicle sensor to prevent excessive accumulation of maturefollicles in Drosophila ovaries and oocyte aging.

Excessive mature follicle accumulation in ovaries harms oocyte health and offspring viability. As such, the number of mature follicles in ovaries is tightly controlled. In Drosophila, each ovary is comprised of [~]16 ovarioles, each containing 1-2 mature follicles, regardless of the females mating status. The mechanism by which the female flies count the number of mature follicles to coordinate egg release and oogenesis remains a mystery. Previous work, along with our RNAseq and antibody analysis, demonstrated that Drosophila insulin-like peptide 8 (DILP8) is expressed in somatic follicle cells of mature follicles but not in younger follicles. Contrary to previous findings, we found that DILP8 is not essential for mating-induced ovulation/egg laying. In contrast, global depletion or follicle-cell-specific knockdown of dilp8 leads to defective ovulation/egg laying and a significant increase of mature follicles in virgin females. In addition, we found that excessive accumulation of mature follicles in dilp8-knockdown females leads to poor oocyte quality. Furthermore, knockdown of Lgr3 (Leucine-rich repeat-containing G protein-coupled receptor 3), encoding a previously identified DILP8 receptor, showed similar ovulation/egg laying defects, accumulation of mature follicles, and poor oocyte quality in virgin females. Therefore, DILP8 functions as a mature follicle sensor to prevent excessive accumulation of mature follicles and maintain oocyte quality through the Lgr3 receptor in virgin females. Because mating is not always available in the wild and the DILP8/Lgr3 pathway is highly conserved across multiple species, our findings suggest that DILP8/Lgr3 is likely critical for maintaining the optimal reproductive fitness of virgin females and for species survival in the wild.

physiology↗

β-Arrestin Condensates Regulate G Protein-Coupled Receptor Function

G protein-coupled receptors (GPCRs) are the largest class of receptors in the genome and control many signaling cascades essential for survival. GPCR signaling is regulated by {beta}-arrestins, multifunctional adapter proteins that direct receptor desensitization, internalization, and signaling. While at many GPCRs, {beta}-arrestins interact with a wide array of signaling effectors, it is unclear how {beta}-arrestins promote such varied functions. Here we show that {beta}-arrestins undergo liquid-liquid phase separation (LLPS) to form condensates that regulate GPCR function. We demonstrate that {beta}-arrestin oligomerization occurs in proximity to the GPCR and regulates GPCR functions such as internalization and signaling. This model is supported by a cryoEM structure of the adhesion receptor ADGRE1 in a 2:2 complex with {beta}-arrestin 1, with a {beta}-arrestin orientation that can promote oligomerization. Our work provides a paradigm for {beta}-arrestin condensates as regulators of GPCR function, with LLPS serving as an important promoter of signaling compartmentalization at GPCRs.

cell biology↗

Unique B Cell and Germinal Center Responses in Mice with Severe versus Mild Orientia tsutsugamushi Infection

The intracellular bacterium Orientia tsutsugamushi (Ot) is the causative agent of scrub typhus, an emerging and neglected tropical disease. Immunity against Ot infection in patients is known to be short-lived, as circulating antibodies can wane around one-year post-infection. However, its underlying mechanisms remain unclear; host immune signatures to clinically prevalent Ot strains are also undefined. In this study, we infected C57BL/6 mice with two clinically prevalent Ot strains with distinct virulence to examine splenic B cell and germinal center (GC) responses. While highly virulent Karp strain-infected mice had 50% mortality rates, intermediate virulent strain Gilliam-infected mice survived, gained body weight, and maintained relatively low bacterial burden levels during infection. Yet, Gilliam infection resulted in strong splenic B cell responses, as judged by absolute cell numbers of total splenic B cells, follicular B cells, and marginal zone (MZ) B cells alongside with significantly higher titers of total IgG and IgM antibodies at the late stage of infection. While altered splenic architecture with increased distance between white pulp regions was detectable in both strains, GC disorganization/collapse and MZ abrogation were only detected in Karp-infected spleens. To define the driving force of GC loss, we compared RNAseq profiles between spleens infected with the Karp or Gilliam strain, and found significantly upregulated inflammation biomarkers (Ccl2, Il33, Ifng) and severe scrub typhus-related inflammatory pathways (Il1, Il6, Tnf, and Ifng) in Karp infection at day 4 (D4, early stage of infection). IPA analysis further showed upregulated neutrophil degranulation and defense response pathways in Karp-infected spleens, while Gilliam-infected spleens showed upregulation of phagocytosis signaling pathways. Flow cytometry confirmed a marked influx of activated myeloid cell subsets (neutrophils, M1 macrophages, and inflammatory monocytes) in the spleen during Karp infection as compared to Gilliam infection, indicating excessive inflammatory infiltration in highly virulent Ot strain infection. Collectively, our findings establish several Ot strain-related immune signatures which help fill the knowledge gap of deficiencies in the host adaptive immune response during acute scrub typhus. Author SummaryThe intracellular bacterium O. tsutsugamushi (Ot) is the etiologic agent of the neglected tropical disease scrub typhus. It is well-known that immunity against Ot infection is short-lived, yet no in-depth studies have examined or compared adaptive immunity or deficiencies at cellular and molecular levels during acute Ot infection with clinically relevant Ot strains. In this study, we used two clinically prevalent Ot strains that cause differential diseases outcomes in the C57BL/6 murine model to examine B cell and germinal center (GC) responses. In sharp contrast to Karp infection, which caused 50% mortality rates by D12, Gilliam infection elicited self-limiting infection with low tissue splenic bacterial burdens. Yet, Gilliam-infected mice demonstrated robust humoral immune responses, as demonstrated by strong IgM and IgG antibody titers at D12 and absolute numbers of splenic B cell subsets at D8 and D12. While both Ot strains altered typical splenic white pulp architecture, only Karp infection abrogated GC and MZ structures. Comparison of RNAseq profiles of Karp-vs. Gilliam-infected spleens revealed several unique features, including Karp infection-associated upregulation of inflammation genes (Ccl2, Il33, Ifng) and inflammatory pathways (Il1, Il6, Tnf, Ifng) at D4, as well as upregulated leukocyte recruitment, neutrophil degranulation, and defense response pathways. In sharp contrast, Gilliam infection upregulated pathways involved in phagocytosis immunoregulatory interactions. Flow cytometry confirmed significant influx and activation of myeloid cell subsets (neutrophils, macrophages, M1 macrophages, monocytes) during Karp infection. Our study reveals unique patterns in the differential immune responses to two clinically prevalent Ot strains and helps understand potential mechanisms of immune alterations during severe scrub typhus.

immunology↗

High-throughput protein target mapping enables accelerated bioactivity discovery for ToxCast and PFAS compounds

Chemical pollution is a global threat to human health, yet the toxicity mechanism of most contaminants remains unknown. Here, we applied an ultrahigh-throughput affinity-selection mass spectrometry (AS-MS) platform to systematically identify protein targets of prioritized chemical contaminants. After benchmarking the platform, we screened 50 human proteins against 481 prioritized chemicals, including 446 ToxCast chemicals and 35 per-and polyfluoroalkyl substances (PFAS). Among 24,050 interactions assessed, we discovered 35 novel interactions involving 14 proteins, with fatty acid-binding proteins (FABPs) emerging as the most ligandable protein family. Given this, we selected FABPs for further validation, which revealed a distinct PFAS binding pattern: legacy PFAS selectively bound to FABP1, whereas replacement compounds, PFECAs, unexpectedly interacted with all FABPs. X-ray crystallography further revealed that the ether group enhances molecular flexibility of alternative PFAS, to accommodate the binding pockets of FABPs. Our findings demonstrate that AS-MS is a robust platform for the discovery of novel protein targets beyond the scope of the ToxCast program and highlight the broader protein-binding spectrum of alternative PFAS as potential regrettable substitutes.

pharmacology and toxicology↗

Respiratory Airway Secretory Cells act as Immune Sentinels in Human Distal Airways

Pulmonary immunity in the human distal respiratory airways is essential for lung function but remains poorly explored, mainly due to limited physiologically relevant models. Here, we develop distal lung organoids containing respiratory airway secretory (RAS) cells, a recently identified epithelial population unique to the distal airways of humans and large mammals, using human pluripotent stem cells (hPSCs). Lineage tracing identified RAS cells as descendants of SOX9brightNKX2-1bright progenitors. Single-cell transcriptomics elucidated that RAS cells exhibited a distinct immune-competent phenotype with enriched genes associated with viral host entry and pattern recognition receptor signaling. Functionally, RAS cells infected by respiratory syncytial virus (RSV) exhibited enhanced antiviral activity marked by upregulation of interferon-stimulated genes (ISGs) and complement component 3 (C3). In contrast, bacterial flagellin or Pseudomonas aeruginosa (PAO1) triggered a TLR5-driven immune response in RAS cells, inducing complement system activation, a response suppressed by selective TLR5 inhibition. Notably, in chronic obstructive pulmonary disease (COPD), RAS cells displayed dysregulated immune activation, characterized by elevated expression of adaptive immune mediators. Together, our findings identify RAS cells as previously unrecognized sensors and effectors of mucosal immunity in the human distal airways and reveal their roles in viral infection, bacterial stimulation, and chronic inflammatory lung disease, providing potential therapeutic targets for respiratory diseases.

cell biology↗

Intrinsic OASL expression licenses interferon induction during influenza A virus infection

Effective control of viral infection requires rapid induction of the innate immune response, especially the type I and type III interferon (IFN) systems. Despite the critical role of IFN induction in host defense, numerous studies have established that most cells fail to produce IFNs in response to viral stimuli. The specific factors that govern cellular heterogeneity in IFN induction potential during infection are not understood. To identify specific host factors that license some cells but not others to mount an IFN response to viral infection, we developed an approach for analyzing temporal scRNA-seq data of influenza A virus (IAV)-infected cells. This approach identified the expression of several interferon stimulated genes (ISGs) within pre-infection cells as correlates of IFN induction potential of those cells, post-infection. Validation experiments confirmed that intrinsic expression of the ISG OASL is essential for robust IFNL induction during IAV infection. Altogether, our findings reveal an important role for IFN-independent, intrinsic expression of ISGs in promoting IFN induction and provide new insights into the mechanisms that regulate cell-to-cell heterogeneity in innate immune activation.

immunology↗

Tresor: An integrated platform for simulating transcriptomic reads with realistic PCR error representation across various RNA sequencing technologies

The rapid advancement of high-throughput sequencing technologies has spurred the development of numerous computational tools designed to identify gene expression patterns from growing datasets at both bulk and single-cell sequencing levels. The recent advent of longread sequencing technologies has further accelerated the availability and refinement of these tools. The lack of ground-truth labels and annotations in sequencing data presents a significant challenge for evaluating the efficacy of analytical tools. To address this, we developed Tresor, an integrated platform for simulating both short and long reads at bulk and single-cell levels. We devised a tree-based algorithm to significantly accelerate in silico experiments at high PCR cycles. Tresor allows for customising sequencing libraries with highly modular and flexible read structures, facilitating the verification of sequencing-related biological discoveries. This tool also includes features that introduce substitution, insertion, and deletion errors at various stages of library preparation, PCR amplification, and sequencing, enhancing its applicability in diverse experimental conditions and simulating real world conditions. Our results demonstrate that, upon removal of PCR duplicates, cell type-specific gene expression profiles derived from our simulated reads highly resemble reference data. We envisage that Tresor will provide valuable insights into a broader range of transcriptomics analyses and support the development of more effective algorithms for read alignment and UMI deduplication.

bioinformatics↗