Biology subjects

Xin, S.

Publications and source records attributed to Xin, S..

13 recordsLinked to original sources

bioRxiv2026

Spatiotemporal Mapping of Tertiary Lymphoid Structure Heterogeneity Shapes Immune Niches and Clinical Outcomes in Intrahepatic Cholangiocarcinoma

Intrahepatic cholangiocarcinoma (iCCA) is a highly lethal malignancy with limited therapeutic options. The spatial architecture and functional diversity of tertiary lymphoid structures (TLSs) in iCCA remain unclear. Here, we present a multimodal spatial atlas of TLSs and identified Intra-tumoral TLSs (iTLSs) as independent prognostic markers. Bulk proteomic profiling of 214 discovery and 155 validation cases identified a four-tier TLS-based TME classification system and supported development of a TLS-predictive random forest classifier. Imaging mass cytometry revealed that iTLS tumors harbor structured immune architectures, where M1-like tissue-resident macrophages (RTMs), dendritic cells, and CXCL13 CD4 T cells co-localize to form antigen-presenting neighborhoods (apc-CNs) spatially coupled to TLS core regions (TLScore-CNs). Single-cell spatial transcriptomics further resolved 61 TLSs into 14 spatial niches and defined a pseudo-temporal maturation continuum: aggregated, activated, and post-activated. Intra-niche communication, primarily mediated by ifnCAFs, iCAFs, and CXCL12 macrophages, evolved dynamically with maturation. Single-nucleus RNA-sequencing combined with Tangram-based spatial mapping revealed CXCL12 macrophages and iCAFs forming a peripheral band in aggregated TLSs, while ifnCAFs infiltrated TLS interiors during activation. These findings define TLS heterogeneity and provide insights for stroma-directed immunotherapy. TeaserAn atlas of tertiary lymphoid structures reveals immune-stroma interactions in Intrahepatic cholangiocarcinoma.

immunology↗

bioRxiv2026

CAR-T-drug conjugate against solid tumor

Chimeric antigen receptor (CAR)-T cell therapy has been clinically successful in hematologic cancers but faces challenges in solid tumors, primarily due to limited tumor infiltration, immunosuppressive tumor microenvironments (TME), and antigen heterogeneity. While combining CAR-T cell therapy with chemotherapy can enhance antitumor activity, this often leads to substantial systemic toxicity. In this study, we introduce CAR-T-drug conjugate (CAR-T-D-C), a new class of dual-functional therapeutics that effectively addresses these obstacles by integrating click chemistry for precise conjugation of cytotoxic agents onto antigen-specific CAR-T cells. By transforming the hostile TME into an ally, this approach facilitates localized delivery of cytotoxic payload directly to the tumor site, enhancing the overall effectiveness of CAR-T therapy in solid tumors. CAR-T-D-Cs with different CAR-T cell binders exhibit robust antitumor activity across diverse solid tumor models, including both human tumor xenografts and syngeneic models. Spatial transcriptomic studies reveals that CAR-T-D-C achieves improved CAR-T tumor infiltration and functional activation within the TME. Compared to conventional CAR-T therapy, CAR-T-D-C markedly enhances immune cell infiltration, augments effector functions, promotes antigen spreading, amplifies systemic immune responses, and improves overall anti-tumor immunity. CAR-T-D-C represents a versatile therapeutic concept that combines the potency of small molecule drugs and the specificity of CAR-T cells as a 2-in-1 immunochemotherapy for treatment of solid tumors.

immunology↗

bioRxiv2025

LGFN: A Dynamic Gating Framework for Lyrics-Audio Alignment in Music Emotion Recognition

Music emotion recognition (MER) is challenging due to the ambiguous nature of audio features. For example, a fast tempo might indicate excitement or anger. To address this issue, we propose the Lyrics-Aware Gate Fusion Network LGFN, a novel cross-modal dynamic fusion approach. This network extracts audio features using ResNet for Mel spectrograms and 1D CNN for waveforms, while leveraging BERT for lyric embeddings. The key innovation of LGFN lies in its attentional alignment layer AAL, which effectively bridges the temporal misalignment between lyrics and audio. Additionally, the dynamic gate fusion module DGFM adaptively adjusts the weight of audio and text features based on their reliability. This allows the model to automatically determine the contribution of each modality, enhancing the accuracy of emotion recognition. Ablation studies on the music emotion recognition datasets MER1101 and DEAM2015 demonstrate the effectiveness of our proposed AAL and DGFM, while visualizing the gate weights offers insights into the models decision-making process. We also conduct comprehensive experiments on different human multimodal emotion recognition benchmarks, which show the superiority of our approach over the state-of-the-arts.

bioengineering↗

bioRxiv2024

Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT

Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for simultaneous co- sequencing of spatial transcriptome and guide RNAs (gRNAs) on the same tissue section for in vivo CRISPR screen with genome-scale gRNA libraries, offering a comprehensive understanding of how genetic modifications affect cellular behavior and tissue architecture. This platform supports a variety of delivery vectors, gRNA library sizes, and tissue preparations, along with two distinct gRNA capture methods, making it adaptable to a wide range of experimental setups. In applying Perturb-DBiT, we conducted un-biased knockouts of tens of genes or at genome-wide scale across three cancer models. We mapped all gRNAs in individual colonies and corresponding transcriptomes in a human cancer metastatic colonization model, revealing clonal dynamics and cooperation. We also examined the effect of genetic perturbation on the tumor immune microenvironment in an immune-competent syngeneic model, uncovering differential and synergistic perturbations in promoting immune infiltration or suppression in tumors. Perturb-DBiT allows for simultaneously evaluating the impact of each knockout on tumor initiation, development, metastasis, histopathology, and immune landscape. Ultimately, it not only broadens the scope of genetic inquiry, but also lays the groundwork for developing targeted therapeutic strategies.

genomics↗

bioRxiv2024

An optimized somatic embryo transformation system assisted homozygous edited rubber tree generation method mediated by CRISPR/Cas9

Previously, we have realized the CRISPR/Cas9-RNP and plasmid mediated protoplast transient transformation genome editing in the rubber tree (Hevea brasiliensis), but no gene editing plants were acquired due to the bottleneck of genetic transformation. In present study, antibiotic sensitivity tests against kanamycin, hygromycin and basta were analyzed for embryo screening, the results demonstrated that 10 mg/L hygromycin is the best for transformation. Then Agrobacterium mediated transformation of H. brasiliensis embryos was carried out using a pCAMBIA1300-based CRISPR/Cas9 vector targeting Phytoene desaturase gene (HbPDS). High-throughput sequencing of T0 generation positive embryos which were used as regeneration materials in typical transformation procedure showed that more than 90% T0 edited embryos are chimeric with a 3.2% editing efficiency. A T0 embryo with 9.8% edited cells was sliced into small pieces for one more cycle embryogenesis to produce T1 generation embryos in order to improve the ratio of homozygous embryos. Subsequently, next-generation sequencing (NGS) demonstrated that 29 out of 33 T1 embryos were edited, nearly 50% of which were found homozygous. At last, besides four chimeric plantlets with partial albino leaves, four plantlets with complete albino phenotype were regenerated from the 29 T1 generation edited embryos, among which one is a homozygous mono-allelic mutant and the other three are homozygous bi-allelic mutants. NGS demonstrated that the threshold for the proportion of edited cells with expected albino phenotype is between 70-85%. Additionally, Tail-PCR indicate that the T-DNA was inserted into different genome positions in the four homozygous edited plantlets, combined with the different genotypes are considered, the four homozygous plantlets can be confirmed as independently derived from single transformed cells. Overall, this is the first edited rubber trees with expected phenotype reported publicly, which shows the potential in genetic improvement of H. brasiliensis by CRISPR/Cas9 gene editing, and subculture of T0 positive transformed somatic embryos into T1 generation is proved to be an effective and necessary procedure to produce homozygous transgenic plantlets. This study presents a significant advancement in transgenic and gene editing for rubber tree.

plant biology↗

bioRxiv2024

High-fidelity enhanced AsCas12a knock-in mice for efficient multiplexed gene editing, disease modeling and orthogonal immunogenetics

The advancement of CRISPR gene editing technology, especially the development of Cas9 knock-in mice, has significantly boosted the functional discovery of various genetics factors in diverse fields including genetics, genomics, immunology, and the biology of cancer. However, the pleiotropic effects on human disease and the complex nature of gene interaction networks require a knock-in mouse model capable of simultaneous multiplexed gene perturbation. Here, we present the generation and applications of Cre-dependent conditional and constitutive high-fidelity, enhanced AsCas12a (enAsCas12a-HF1) Rosa26-knock-in mice in the C57BL/6 background. With these mouse strains, we demonstrate highly efficient and multiplexed in vivo and ex vivo genome engineering as applied to lipid nanoparticle (LNP)-RNA-based liver protein targeting, AAV-based tumor modeling, and retrovirus-based immune cell engineering. By integrating with a dCas9-SPH CRISPR activation transgenic strain, we establish a simultaneous dual gene activation and knockout (DAKO) system that showcases the modular potential of these enAsCas12a-HF1 mice. Importantly, constitutive expression of enAsCas12a-HF1 does not lead to any discernable pathological differences as compared to the C57BL/6 background strain. These knock-in mice and the accompanying delivery methods would empower the deconvolution of complex gene interaction networks in broad areas of research.

bioengineering↗

bioRxiv2024

Genome scale CRISPR screens identify actin capping proteins as key modulators of therapeutic responses to radiation and immunotherapy

Radiotherapy (RT), is a fundamental treatment for malignant tumors and is used in over half of cancer patients. As radiation can promote anti-tumor immune effects, a promising therapeutic strategy is to combine radiation with immune checkpoint inhibitors (ICIs). However, the genetic determinants that impact therapeutic response in the context of combination therapy with radiation and ICI have not been systematically investigated. To unbiasedly identify the tumor intrinsic genetic factors governing such responses, we performed a set of genome-scale CRISPR screens in melanoma cells for cancer survival in response to low-dose genotoxic radiation treatment, in the context of CD8 T cell co-culture and with anti-PD1 checkpoint blockade antibody. Two actin capping proteins, Capza3 and Capg, emerged as top hits that upon inactivation promote the survival of melanoma cells in such settings. Capza3 and Capg knockouts (KOs) in mouse and human cancer cells display persistent DNA damage due to impaired homology directed repair (HDR); along with increased radiation, chemotherapy, and DNA repair inhibitor sensitivity. However, when cancer cells with these genes inactivated were exposed to sublethal radiation, the persistence of DNA damage promoted activation of the STING pathway, induction of inhibitory CEACAM1 ligand expression and resistance to CD8 T cell killing. Patient cancer genomics analysis reveals an increased mutational burden in patients with inactivating mutations in CAPG and/or CAPZA3, at levels comparable to other HDR associated genes. There is also a positive correlation between CAPG expression, CD8 T cell tumor infiltration and response to immunotherapy among patient datasets. Our results unveil the critical roles of actin binding proteins for efficient HDR within cancer cells and demonstrate a previously unrecognized regulatory mechanism of therapeutic response to radiation and immunotherapy.

genetics↗

bioRxiv2023

Integrative analysis of multi-omics and machine learning highlighted an m6A-related mRNA signature as a robust AAA progression predictor

ObjectiveAbdominal aortic aneurysm (AAA) is a life-threatening disease in vascular surgery with significant morbidity and mortality rates upon rupture. Despite surgical interventions, effective targeted drugs for non-surgical candidates are lacking. M6A methylation, a dynamic RNA modification, has been implicated in various diseases, but its role in AAA remains poorly understood. In this study, we aimed to explore the participation of M6A in the progression of AAA progression through multi-omics and machine learning. Approach and Resultswe conducted methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-seq) to profile the m6A methylome in AAA tissues, identifying differentially methylated genes (DMGs). Integrating multi-omics data from RNA-sequencing (RNA-seq) in GEO databases, we developed a machine learning-based AAA m6A-related mRNA signature (AMRMS) to predict AAA dilation risk. The AMRMS demonstrated robust predictive performance in distinguishing AAA patients with large AAA and small AAA. Notably, the AMRMS highlighted FKBP11 as a key gene with a significant impact on the predicted model. Subsequent single-cell RNA sequencing (ScRNA-seq) revealed the pivotal role of FKBP11-positive plasma cells in AAA progression. ConclusionsOur study provides novel insights into the regulatory role of m6A modification in AAA pathogenesis, and further develop a promising AMRMS for risk evaluation in AAA patients. Furthermore, the identification of FKBP11 positive plasma cells as significant contributors to AAA progression opens new avenues for targeted therapeutic interventions.

bioinformatics↗

bioRxiv2023

Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition

BackgroundThe endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis in vertebrate is highly conserved. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse. ResultsWe reconstructed the single-cell EHT trajectories of human and mouse, and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories. Enhanced TE activation was tightly associated with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate the emergence of hematopoietic stem cells. Furthermore, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Additionally, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential enhancers derived by TEs, which may boost the expression of specific EHT marker genes. ConclusionsOur study provides a systematic vision on how TEs are dynamically controlled to promote the hematopoietic fate decision through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent hematopoietic stem cells.

bioinformatics↗

bioRxiv2022

Reactive astrocyte derived extracellular vesicles promote functional repair post stroke

Reactive astrocytes are both neurotoxic and pro-regenerative. Their reparative roles after injury have been demonstrated, but how they play a contributing role to regeneration remains question. Here, we investigate the use of astrocytic extracellular vesicles from primary astrocytes cultured in reactive conditions in promoting repair after ischemic stroke. Our studies show that extracellular vesicles derived from reactive astrocytes that co-express a significant number of reactive genes (155 upregulated including log2 of 9.61 for Lcn2) and axonal outgrowth genes (59 upregulated including log2 of 3.49 Ntn1) are necessary for improved regenerative outcomes, including axonal infiltration, vascularization, and improved behavioral recovery. Proteomic analysis of the extracellular vesicles show that astrocytes enrich pro-reparative proteins in extracellular vesicles with only 30 proteins relating to inflammatory or complement pathways loaded out of a total of 1073 proteins. Further, we show that the use of a biomaterial scaffold is necessary for the improved regeneration observed from reactive astrocyte extracellular vesicles. These studies show that reactive astrocytes use extracellular vesicles enriched with pro-repair proteins to promote recovery after injury.

neuroscience↗

bioRxiv2020

NF45/NF90-mediated rDNA transcription provides a novel target for immunosuppressant development

Herein, we demonstrate that NFAT, a key regulator of the immune response, translocates from cytoplasm to nucleolus and interacts with NF45/NF90 complex to collaboratively promote rDNA transcription via triggering the directly binding of NF45/NF90 to the ARRE2-like sequences in rDNA promoter upon T cell activation in vitro. The elevated pre-rRNA level of T cells is also observed in both mouse heart or skin transplantation models, and in kidney transplanted patients. Importantly, T cell activation can be significantly suppressed by inhibiting NF45/NF90-dependent rDNA transcription. Amazingly, CX5461, a rDNA transcription specific inhibitor, outperformed FK506, the most commonly used immunosuppressant, both in terms of potency and off-target activity (i.e. toxicity), as demonstrated by a series of skin and heart allograft models. Collectively, this reveals NF45/NF90-mediated rDNA transcription as a novel signaling pathway essential for T cell activation and as a new target for the development of safe and effective immunosuppressants.

molecular biology↗

bioRxiv2019

Immune Landscape of Invasive Ductal Carcinoma Tumour Microenvironment Identifies a Prognostic and Immunotherapeutically Relevant Gene Signature

BackgroundInvasive ductal carcinoma (IDC) is a clinically and molecularly distinct disease. Tumour microenvironment (TME) immune phenotypes play crucial roles in predicting clinical outcomes and therapeutic efficacy.\n\nMethodIn this study, we depict the immune landscape of IDC by using transcriptome profiling and clinical characteristics retrieved from The Cancer Genome Atlas (TCGA) data portal. Immune cell infiltration was evaluated via single-sample gene set enrichment (ssGSEA) analysis and systematically correlated with genomic characteristics and clinicopathological features of IDC patients. Furthermore, an immune signature was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm. A random forest algorithm was applied to identify the most important somatic gene mutations associated with the constructed immune signature. A nomogram that integrated clinicopathological features with the immune signature to predict survival probability was constructed by multivariate Cox regression.\n\nResultsThe IDC were clustered into low immune infiltration, intermediate immune infiltration, and high immune infiltration by the immune landscape. The high infiltration group had a favourable survival probability compared with that of the low infiltration group. The low-risk score subtype identified by the immune signature was characterized by T cell-mediated immune activation. Additionally, activation of the interferon- response, interferon-{gamma} response and TNF- signalling via the NF{kappa}B pathway was observed in the low-risk score subtype, which indicated T cell activation and may be responsible for significantly favourable outcomes in IDC patients. A random forest algorithm identified the most important somatic gene mutations associated with the constructed immune signature. Furthermore, a nomogram that integrated clinicopathological features with the immune signature to predict survival probability was constructed, revealing that the immune signature was an independent prognostic biomarker. Finally, the relationship of VEGFA, PD1, PDL-1 and CTLA-4 expression with the immune infiltration landscape and the immune signature was analysed to interpret the responses of IDC patients to immune checkpoint inhibitor therapy.\n\nConclusionTaken together, we performed a comprehensive evaluation of the immune landscape of IDC and constructed an immune signature related to the immune landscape. This analysis of TME immune infiltration patterns has shed light on how IDC respond to immune checkpoint therapy and may guide the development of novel drug combination strategies.

cancer biology↗

bioRxiv2018

Immunogenicity and protective potency of Norovirus GII.17 virus-like particle-based vaccine

Noroviruses (NoVs) are a major cause of acute viral gastroenteritis in adults and children worldwide. Lacking of cell culture system and animals models that must be considered the virus like particles (VLPs) used as an effective vaccine development. In the present study, we investigated the expression of the major capsid protein (VP1) of Genogroup II, genotype 17 (GII.17) NoV using recombinant baculovirus system in insect cells and saliva binding blockade assay to detect their protective potency. Our results showed that GII.17 VLPs could be successfully generated in sf9 insect cells and electron microscopic revealed that GII.17 VLPs was visualized as spherical particles of -35nm in diameter. Immunized mouse with purified VLPs produced GII.17 specific sera and could efficiently block GII.17 VLPs binding to saliva histo-blood group antigens (HBGAs). Together, these results suggested that GII.17 VLPs represent a promising vaccine candidate against NoV GII.17 infection and strongly support further preclinical and clinical studies.

immunology↗