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Qin, Q.

Publications and source records attributed to Qin, Q..

At least 19 recordsLinked to original sources
bioRxiv2026

TRIM52 downregulates IFN-β production by targeting TBK1 for proteasome degradation.

The IFN-I (type I interferon) signaling pathway is the first line of defence against foreign pathogens. Stringent control of signalling pathways is necessary to maintain host immune responses and homeostasis. However, the underlying mechanism for its tight regulation is yet completely understood. In this study, we demonstrated that the TRIM family protein tripartite motif-containing 52 (TRIM52) is a novel negative regulator of IFN-{beta} production. Ectopically expressed TRIM52 markedly inhibited the activation of the IFN-{beta} promoter by ectopic expression of cGAS/STING, RIG-IN, or TRIF, MAVS, STING, and TBK1 but not by IRF3/5D, indicating that TRIM52 targets TBK1. TRIM52 also significantly inhibited the IFN-{beta}, ISG54, and ISG56 production, the dimerization of IRF3 and the nuclear localization of IRF3-YFP induced by ectopic expression of TBK1. Co-immunoprecipitation experiment revealed that TRIM52 specifically interacted with TBK1. Furthermore, the TBK1 protein, but not its mRNA, decreased considerably with increasing expression of TRIM52, and TRIM52 did not decrease the expression of the cGAS, STING, or IRF3 proteins. In addition, proteasome inhibitor MG-132 blocked the reduced TBK1 induced by TRIM52, indicating that TRIM52 caused TBK1 degradation via the proteasome pathway. Co-IP and ubiquitination assays demonstrated that TRIM52 promotion of K48-linked ubiquitination of TBK1, which depends on its E3 ubiquitin ligase. Collectively, our findings identify a previously unrecognized role of TRIM52 in regulating the IFN-I signalling pathway through targeting TBK1 for polyubiquitination and degradation.

immunology↗
bioRxiv2026

AlaRS-mediated lactylation shields PARP1 from ubiquitination to promote HNSCC progression

Abstract textMetabolic reprogramming in solid tumors causes massive lactate accumulation, yet how this drives oncogenesis remains incompletely understood. Here, we identify alanyl-tRNA synthetase (AlaRS) as a cellular lactyltransferase that promotes head and neck squamous cell carcinoma (HNSCC) progression. AlaRS directly catalyzes site-specific lactylation of the DNA repair protein PARP1 at lysines K249 and K667. Crucially, we uncover a competitive post-translational crosstalk wherein this lactylation directly antagonizes PARP1 ubiquitination. This "lactyl-shield" prevents proteasomal degradation, hyper-stabilizing the PARP1-Mortalin complex and sustaining tumor proliferation via p53/p21 dysregulation. To therapeutically exploit this mechanism, we identified chelerythrine (CHE) as a potent, selective inhibitor that directly binds the AlaRS catalytic center. CHE abrogates AlaRS lactyltransferase activity, destabilizes PARP1, and robustly suppresses HNSCC xenograft growth in vivo. These findings establish a novel metabolic-post-translational axis linking lactate accumulation to oncoprotein stabilization, providing a blueprint for targeting tRNA synthetase moonlighting functions in cancer.

molecular biology↗
bioRxiv2026

Sphk1-S1P signaling drives blood-brain barrier breakdown after intracerebral hemorrhage via HIF-1α-dependent upregulation of Bsg-MMP-9

Blood-brain barrier (BBB) breakdown is a critical pathological event driving secondary brain injury and poor outcomes following intracerebral hemorrhage (ICH). However, the mechanisms governing acute BBB breakdown after ICH remain incompletely understood. Here we demonstrate that the Sphk1-S1P-S1PR3 signaling plays a pivotal role in this process. Sphk1 expression was significantly upregulated in the perihematomal endothelial cells of both ICH patients and mice, with levels positively correlating with BBB dysfunction severity and poor clinical outcomes. Using endothelial-specific genetic gain- and loss-of-function approaches, we found that Sphk1 knockdown attenuated BBB leakage, reduced hematoma volume and brain edema, preserved tight junction integrity, and improved neurological function at 1-day post-ICH, whereas Sphk1 overexpression exacerbated these pathological features. Mechanistically, transcriptomic profiling of perihematomal endothelial cells revealed that prior to its established role in Nlrp3-mediated pyroptosis, Sphk1 promotes early BBB breakdown by regulating the Bsg-MMP-9 axis. Endothelial-specific Bsg deletion completely abrogated the deleterious effects of Sphk1, confirming Bsg as an indispensable intermediary through which Sphk1 signals to MMP-9. ATAC-seq and dual-luciferase assays further demonstrated that Sphk1-generated S1P signals through S1PR3 to activate HIF-1, which directly binds the Bsg promoter to drive its transcription, ultimately promoting MMP-9-mediated tight junction degradation. These findings delineate a complete hierarchical signaling cascade from metabolic enzyme to transcriptional regulation and subsequent barrier injury, establishing the Sphk1-Bsg-MMP-9 axis as a promising therapeutic target for ICH. One sentence summaryThis work identifies an early and pivotal mechanism of blood-brain barrier breakdown after intracerebral hemorrhage, demonstrating that Sphk1-generated S1P signals through S1PR3 to activate HIF-1, which directly transactivates Bsg expression, leading to MMP-9-mediated tight junction degradation, thereby establishing a novel hierarchical axis with therapeutic potential.

cell biology↗
bioRxiv2026

LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads

Long-read sequencing is a powerful technique capturing multiple variants within single continuous reads. This length allows individual reads to bridge small and structural variants while carrying crucial phasing information. However, current computational tools treat small variant calling, structural variant (SV) detection and phasing as largely disconnected problems, failing to unleash the full potential of long reads. Here, we present longcallD, a unified framework utilizing local multiple-sequence alignment to simultaneously call and phase small and structural variants. By integrating germline phasing and retrotransposition hallmarks, longcallD also identifies low-fraction mosaic variants and detects mobile element insertions supported by a single read. Compared to existing methods, our unified approach substantially improves SV discovery and mosaic variants accuracy while maintaining competitive small variant calling. We anticipate that longcallD will provide a robust foundation for resolving complex genetic architectures in clinical and evolutionary applications.

genomics↗
bioRxiv2026

Fibroblasts neurotrophin signaling sustains pathological vascular maturation in rheumatoid arthritis.

Treatment failures in rheumatoid arthritis (RA) leads to undesirable morbidity associated with immunosuppression. Recent studies of synovial tissue from refractory RA patients highlight the role of synovial fibroblasts and vascular endothelium in driving treatment failure. Utilizing high-dimensional spatial transcriptomics, we uncovered a crucial role for neurotrophin signaling in driving abnormal vascular maturation in RA synovia. Neurotrophins, including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT3), induce differentiation of synovial fibroblasts into mural cells - pericytes and vascular smooth muscle cells. Mechanistically, NOTCH3 signaling activates a cascade of neurotrophin signaling through transcriptional induction of NGFR, a co-receptor for NGF. In RA synovial tissue explants, stimulation with NGF, BDNF, or NT3 leads to a dramatic increase in maturation of synovial tissue vasculature. Conversely, pharmacologic inhibition with neurotrophin inhibitors drastically abolished maturation of vascularization in RA synovial explants. Notably, the FDA-approved tropomyosin receptor kinase (TRK) inhibitors larotrectinib and entrectinib effectively reverse synovial vascular maturation in human RA tissue explants.Our findings suggest that fibroblast-derived neurotrophin signaling is a critical pathway in sustaining mature blood vessels in RA synovia, and that neurotrophin inhibitors reverse abnormal vascular maturation in RA. One Sentence SummaryIn rheumatoid arthritis, fibroblast neurotrophin signaling drives abnormal vascular maturation by inducing differentiation of fibroblasts into vascular mural cells.

molecular biology↗
bioRxiv2025

Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes

Somatic structural variants (SVs) play a crucial role in tumor development and evolution, yet their identification remains challenging, partly due to limitations in current reference genomes. We present a systematic evaluation of diploid donor-specific assemblies (DSAs)--generated based on hybrid long-read sequencing data--as the reference genome for detecting somatic SVs. We analyzed six tumor-normal cell line pairs, using the EchoSV tool we developed to consolidate haplotype-based SVs into a single DSA-based set and to compare SVs across reference genomes. Across Illumina, PacBio HiFi, and Oxford Nanopore Technology (ONT) data, DSA-based analysis improved read-mapping quality, identified over 20% additional SVs compared to GRCh38 and CHM13, and reduced germline artifacts. Most DSA-specific SVs were isolated deletions or insertions in repetitive elements, especially in satellite regions. By tracking sequence-context differences, we identified scenarios in which DSAs enabled detection of SVs missed on GRCh38/CHM13, and confirmed their functional impact with RNA-seq. These results highlight the value of integrating diploid DSAs into somatic SV analysis.

genomics↗
bioRxiv2025

Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly

Accurate detection of mosaic and somatic structural variants (SVs) provides early diagnostic and therapeutic evidence for cancers. While long-read whole-genome sequencing leads to more accurate SV detection than short read sequencing, existing long-read SV callers only look at alignment against a single reference genome and are susceptible to systematic false discovery caused by germline differences between the individual genome and the reference genome. Here we develop a new SV calling method that jointly considers the alignment against a pangenome and the de novo assembly of the germline genome. It dramatically reduces false positive mosaic SVs in normal samples and somatic SVs in cancer cell lines with little loss in sensitivity. Our study highlights the essential need for pangenome or personal genome assembly to integrate SV calls for both SV discoveries and clinical diagnostics. SignificanceWe introduced a novel long-read SV calling method that leverages pangenome and personal genome and greatly improves the accuracy of somatic SV calling.

genomics↗
bioRxiv2025

FuFiHLA: A tool for Full-Field HLA typing from long read data

0.MotivationAllele typing for Human Leukocyte Antigen (HLA) genes has many important clinical applications. Popular short-read typing can only accurately distinguish alleles at the peptide level, which potentially limit our understanding of the effect of variants in non-coding region. Recently, a few methods were declared to distinguish full-field HLA alleles from de-novo assemblies, which motivates us to develop an accurate HLA typing method directly from long reads. ResultsWe developed FuFiHLA, a lightweight open-source software, to type HLA alleles. Currently it supports typing alleles of six HLA genes (HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, and HLA-DQB1) from long reads. Evaluation using 47 PacBio HiFi samples from HPRC shows that FuFiHLA achieves 99.57% accuracy in the full field allele typing and QV as 50.1 for consensus allele sequence construction. Additional testing on four Nanopore R10 reads demonstrates slightly reduced accuracy in the fourth field. Availability and implementationFuFiHLA is available on GitHub (https://github.com/jingqing-hu/FuFiHLA) under MIT License.

bioinformatics↗
bioRxiv2025

A Tonic Signaling Code Predicts CAR-T Cell Efficacy in Diffuse Midline Glioma

Diffuse midline glioma (DIPG/DMG) is a uniformly fatal pediatric brain tumor with no effective cure. Although CAR T-cell therapy shows promise, clinical outcomes remain inconsistent due to limited persistence and premature exhaustion. Reliable predictive biomarkers are lacking, and proposed exhaustion or stemness markers provide limited utility. Here, we systematically compare multiple CAR-T constructs targeting clinically-relevant antigen B7-H3 and identify antigen-independent CAR activation, or tonic signaling, as a key determinant of therapeutic performance. We find that B7-H3 CAR-T cells with restrained tonic signaling display superior tumor killing, persistence, and resistance to exhaustion, along with reduced CAR membrane clustering, in patient-derived DIPG models. Integrated multi-omics and single-cell profiling further reveal a CAR-T tonic signaling-associated gene signature that outperforms conventional exhaustion or stemness markers in predicting therapeutic efficacy across multiple clinical trials, including DIPG and other tumor types. Together, these findings define a mechanistic and predictive framework to guide CAR design and improve clinical outcomes.

cancer biology↗
bioRxiv2025

Type one protein phosphatases (TOPPs) catalyze EIN2 dephosphorylation to regulate ethylene signaling in Arabidopsis

TOPPs (Type one protein phosphatases) widely modulate plant hormone signaling and stress responses in plants, but their roles in ethylene signal transduction remain unknown. This study reveals a reciprocal regulatory relationship between TOPPs and EIN2 (Ethylene insensitive 2)-mediated ethylene signaling. We identified that ethylene can induce TOPPs expression, and topp1/4/5 triple mutants exhibited partial ethylene insensitivity with reduced EIN3 protein levels and ERF1 (Ethylene response factor 1) expression. Mechanistically, TOPPs genetically act upstream of EIN2, physically interacting with its carboxyl-terminal domain (EIN2-C) to dephosphorylate the critical S655 residue. This site-specific dephosphorylation promotes EIN2 stability and EIN2-C nuclear accumulation, thereby activating ethylene responses. Notably, transgenic plants expressing phosphorylation-deficient EIN2S655A displayed constitutive ethylene responses and improved salt tolerance. Further investigation showed that EIN3/EIL1 (EIN3 like 1) transcriptionally activates TOPPs expression by binding to their promoter, amplifying ethylene signaling accordingly. Together, our finding establishes TOPPs play an important regulatory role in ethylene signal transduction and elucidate a dephosphorylation-switch mechanism in controlling EIN2 function, providing critical insight into the role of EIN2 post-translational modifications in plant stress adaptation.

plant biology↗
bioRxiv2025

Structural and temporal dynamics analysis on PANoptosis in sepsis: a bibliometric analysis

PANoptosis, as a new type of programmed cell death, is characterized by pyroptosis, apoptosis and necroptosis, and is a key mechanism causing a variety of inflammatory diseases. Despite the growing number of studies indicating the crucial role of PANoptosis in sepsis, there has been no bibliometric analysis of the research hotspots and trends in this field. Therefore, this study aims to explore the history, research hotspots and emerging trends of PANoptosis in sepsis related research in the past 20 years from the perspective of structure and temporal dynamics. The articles related to PANoptosis in sepsis were retrieved from the Web of Science Core Collection (WoSCC) database from 2000 to 2024. CiteSpace and HistCite were used to analyse the historical features, the evolution of active topics, and emerging trends about PANoptosis in sepsis. 6165 original articles and reviews on PANoptosis in sepsis were included in the bibliometric analysis. In the last 20 years, the number of published documents is increasing year by year and reaches a peak in 2022. At the same time, many activation themes have emerged at different times, as evidenced by a total of 96 categories, 865 keywords and 629 reference bursts. Keyword clustering anchored eight emerging research subfields, namely 0# oxidative stress, 1#pyroptosis, 2#sepsis-associated encephalopathy, 3#acute kidney injury, 4#immunosuppression, 5#necroptosis, 7#lung injury and 8#extracellular vesicles. The keyword alluvial map shows that the most persistent research concepts in this field are phosphatase. And the emerging keywords are toll_like_receptors, regulatory T cells, recognition, etc. In a timeline visualization based on the time span of the citations, we find five relevant emerging topics, namely 1# immunosuppression, 2# sepsis-induced cardiomyopathy, 3# pyroptosis, 4# acute kidney injury, and 13# COVID-19. Our study provides a comprehensive bibliometric analysis and summary about the current status and trends on PANoptosis in sepsis, which will aid researchers in conducting further scientific research in this field.

bioinformatics↗
bioRxiv2025

Robust inference and widespread genetic correlates from a large-scale genetic association study of human personality

Personality traits describe stable differences in how individuals think, feel, and behave and how they interact with and experience their social and physical environments. We assemble data from 46 cohorts including 611K-1.14M participants with European-like and African-like genomes for genome-wide association studies (GWAS) of the Big Five personality traits (extraversion, agreeableness, conscientiousness, neuroticism, and openness to experience), and data from 51K participants for within-family GWAS. We identify 1,257 lead genetic variants associated with personality, including 823 novel variants. Common genetic variants explain 4.8%-9.3% of the variance in each trait, and 10.5%-16.2% accounting for measurement unreliability. Genetic effects on personality are highly consistent across geography, reporter (self vs. close other), age group, and measurement instrument, and we find minimal spousal assortment for personality in recent history. In stark contrast to many other social and behavioral traits, within-family GWAS and polygenic index analyses indicate little to no shared environmental confounding in genetic associations with personality. Polygenic prediction, genetic correlation, and Mendelian randomization analyses indicate that personality genetics have widespread, potentially causal associations with a wide range of consequential behaviors and life outcomes. The genetic architecture of personality is robust and fundamental to being a human.

genomics↗
bioRxiv2025

Moisture Controls on Hydrogen Oxidizing Bacteria: Implications for the Global Soil Hydrogen Sink

Assessing the impact of increasing anthropogenic H2 emissions on Earths radiative balance depends on understanding the soil microbial H2 sink--the largest and the most uncertain term in the global H2 budget. A primary control regulating the soil sink is soil moisture, with a relationship that remains poorly constrained. Here, we assess the sensitivity of microbial H2 oxidation to soil moisture in laboratory experiments with three temperate soils--silty loam, sandy loam, and loamy sand. Using genome-resolved metagenomics, we link H2 oxidation dynamics in these soils to specific microbial taxa adapted to withstand desiccation that have differential contributions to H2 uptake along the moisture gradient. The experiments reveal a notably low moisture threshold for H2 oxidizer activity, at water potentials between -70 and -100 MPa across all soil types, including in an arid sandy soil. These measurements, which represent some of the lowest water potentials reported for soil microbial activity, point to atmospheric H2 as a vital resource for microbial survival under stressful conditions. Through global simulations, we further show that the low moisture threshold for microbial activation increases the contribution of arid and semi-arid regions for soil H2 uptake by 4-7pp, while decreasing the contribution of temperate and continental regions (-7pp), even when assuming a linear scaling between uptake potential and soil organic carbon, as suggested by our experiments. Our results highlight the importance of H2 uptake under extreme hydrological conditions, particularly the roles of desertification, dryland expansion, and H2-oxidizer ecophysiology in modulating long-term changes in H2 uptake.

microbiology↗
bioRxiv2025

Rapid optimization of protein function in mammalian cells via microbe-independent deep assembly and screening

Random mutagenesis and deep mutational scanning (DMS) are widely used to optimize proteins by oversampling large libraries in microbial cells, selecting cells expressing favorable variants, and sequencing to identify enriched variants. However, these methods are slow and costly, require effort to establish selection methods for a given protein function, and do not yield data on lower-performing variants. Here, we describe Microbe-Independent Deep Assembly and Screening (MIDAS), a rapid, high-throughput method for optimizing protein function directly in mammalian cells. As a demonstration, we applied MIDAS to improve a newly designed neurotransmitter bioluminescent indicator (NeuBI) for acetylcholine (ACh). MIDAS systematically optimized interdomain linkers, identified mutational hotspots, and exhaustively scanned amino acid combinations, in each case relating specific sequences to protein performance. MIDAS-optimized variants exhibited improved performance in vivo, highlighting the potential of MIDAS for improving protein function in mammalian systems.

bioengineering↗
bioRxiv2025

The critical role of the ZBP1-NINJ1 axis and IRF1/IRF9 in ethanol-induced cell death, PANoptosis, and alcohol-associated liver disease

Innate immunity provides the critical first line of defense against infection and sterile triggers. Cell death is a key component of the innate immune response to clear pathogens, but excessive or aberrant cell death can induce inflammation, cytokine storm, and pathology, making it a central molecular mechanism in inflammatory diseases. Alcohol-associated liver disease (ALD) is one such inflammatory disease, but the specific innate immune mechanisms driving pathology in this context remain unclear. Here, by leveraging RNAseq and tissue expression in clinical samples, we identified increased expression of the innate immune sensor Z-DNA binding protein (ZBP1) in patients with ALD. We discovered that ZBP1 expression correlated with ALD progression in patients, and that ethanol induced ZBP1-dependent lytic cell death, PANoptosis, in immune (macrophages, monocytes, Kupffer cells) and non-immune cells (hepatocytes). Mechanistically, the interferon regulatory factors (IRFs) IRF9 and IRF1 upregulated ZBP1 expression, allowing ZBP1 to sense Z-NAs through its Z2 domain and drive PANoptosis signaling, cell membrane rupture through NINJ1, and DAMP release. Furthermore, the expressions of ZBP1 and NINJ1 were upregulated in both liver and serum samples from patients with ALD. In mouse models of chronic and acute ALD, ZBP1-deficient mice were significantly protected from disease pathology and liver damage. Overall, our findings establish the critical role of the ZBP1-NINJ1 axis regulated by IRFs in driving inflammatory cell death, PANoptosis, in liver cells, suggesting that targeting these molecules will have therapeutic potential in ALD and other inflammatory conditions.

immunology↗
bioRxiv2024

Deep generative design of neutralizing nanobodies againstSARS-CoV-2 variants

In recent years, single-domain heavy chain antibodies (nanobodies), with only one-tenth the molecular weight of conventional antibodies, have emerged as important therapeutic proteins in the fight against SARS-CoV-2. However, the rapid mutation of the virus often renders existing nanobodies ineffective, underscoring the need to develop nanobodies that specifically target new variants. Traditional methods for discovering nanobodies are time-consuming and complex, making it difficult to efficiently identify nanobodies that bind to specific epitopes. To address this, we propose a de novo nanobody design method based on a Generative Adversarial Network (GAN). We developed a deep generative model, AiCDR, which consists of three discriminators and one generator. By determining the contribution of these three discriminators to the entire network, we can enhance the discrimination of generated sequences and reduce the similarity of the generated CDR3 sequences with natural peptides and random sequences, thereby ensuring their nature-like properties. These generated CDR3 sequences were then grafted onto humanized nanobody scaffolds, resulting in a structural library of approximately 104 nanobodies with natural-like properties. Using computational methods, we screened this library against the Spike (S) protein of the SARS-CoV-2 Omicron variant and identified 10 candidate nanobodies. Functional assays confirmed that two of these nanobodies exhibited neutralizing activity against the S protein. Our study demonstrates the potential of deep learning in nanobody design and offers a novel approach for developing nanobodies that target rapidly evolving viral variants.

bioinformatics↗
bioRxiv2024

Long-range somatic structural variation calling from matched tumor-normal co-assembly graphs

The accurate identification of somatic structural variants (SVs) is a problem with significant applications to clinical cancer research. Though technologies such as long-read sequencing have facilitated the development of more accurate SV calling methods, existing somatic SV callers still struggle with achieving high precision. In this work, we present colorSV, a long-read-based method for calling long-range SVs by examining the local topology of joint assembly graphs from matched tumor-normal samples. colorSV is the first somatic SV calling method that uses a co-assembly approach, as well as the first SV caller that identifies variants by examining characteristics of the assembly graph itself. We demonstrate near-perfect precision and sensitivity for calling translocations on the COLO829 cell line, outperforming four existing somatic SV callers (Severus, Sniffles2, nanomonsv, and SAVANA) in both metrics. We also evaluated colorSV for calling translocations on the HCC1395 cell line, finding that our method achieved a good balance between sensitivity and precision (where the sensitivity was only outperformed by Severus, and the precision was only outperformed by nanomonsv). Our work establishes a novel joint assembly-based strategy for characterizing long-range somatic variation, which could be further expanded or modified for the identification of SVs of different types and sizes.

bioinformatics↗