Biology subjects

Li, Q.

Publications and source records attributed to Li, Q..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

Glycosylated IgG antibodies accelerated the recovery of haemorrhagic fever with renal syndrome patients

AbstractHaemorrhagic fever with renal syndrome (HFRS) is a fatal disease caused by Hantaan virus (HTNV) infection. Humoral immunity is essential for effective viral clearance, however, the glycosylation characteristics of immunoglobulin G (IgG) in HFRS patients is not well known. Peripheral blood mononuclear cells from HFRS patients were obtained for B subset analysis using scRNA-seq and flow cytometry. HTNV specific IgG antibody titers were detected by enzyme-linked immunosorbent assay, and IgG glycosylation was analyzed by ultra-performance liquid chromatography. The proportions of the antibody-secreting memory (ASM) B cells and plasmablasts (PB) were significantly expanded among acute HFRS patients. We discovered significantly increased fucosylated IgG and decreased bisecting N-acetylglucosamine during the convalescent phase of HTNV infection. Meanwhile, positive correlations were observed between ASM subsets and galactosylation/sialylation in the IgG Fc region, and between PB subsets and sialylation. Notably, the glycosylation-related genes, such as RPN1 and RPN2, were primarily expressed differentially in the ASM and PB subclusters which were enriched in the N-glycosylation modifications of proteins through asparagine. Our findings indicated that IgG N-glycosylation may play a crucial role in combating HTNV infection and contributing to clinical recovery, which provided new insights for optimizing glycoengineered therapeutic antibodies.

immunology↗

bioRxiv2025

Tracing the stemness and malignant transition in a heritable colorectal cancer Lynch Syndrome by single-cell RNA-seq analysis

BackgroundLynch Syndrome (LS) is an autosomal dominant disease characterized by germline heterozygous mutations in DNA mismatch repair (MMR) genes. High-risk LS patients may proceed to colorectal cancer (CRC). However, the drivers or biomarkers of LS benign colon tissue approaching malignant CRC are not completely understood. The similarity and difference between LS-related and nonLS-related CRC are also not well interrogated (LS-CRC vs. nonLS-CRC). This study aimed to understand the cellular changes during malignant transition in LS. MethodsSingle-cell RNA sequencing (scRNA-seq) was used to analyze paired biopsy samples from 3 patients with LS (cancer tissues vs. adjacent normal tissues, n=3). Single-nuclear RNA sequencing (snRNA-seq) was used to analyze a frozen biopsy sample from a patient with LS (n=1). scRNA-seq or snRNA-seq datasets from CRC were downloaded from the open source. Integrative computational analysis was performed to conclude the distinct pattern in the single-cell atlas. Immuno-histo-fluorescence staining (IHF) were also performed for three key markers. ResultsIn the single-cell atlas, we observed an increase in primitive cancer stem-cell-like cells with high expression of a general cancer biomarker CarcinoEmbryonic Antigen-related Cell Adhesion Molecule 5 (CEACAM5) in the epithelium of the LS. Infiltration of immune cells and DNA repair biological activity are dramatically increased in LS carcinoma. The burden in LS is fundamentally elevated compared to that in CRC or healthy donors when the mutations are in the coding-sequence-wide range. Furthermore, T cell and macrophage-related tumor immunity is readily mobilized in carcinomas compared to paraCArcinomas. ConclusionsThis study provides single-cell transcriptomic resource using affected tissues from patients with Lynch Syndrome and describes an integrative profile covering the alterations (cancer stem cell markers, mutation burden, and tumor immunity) during the malignant transition from healthy to Lynch Syndrome and to colorectal cancer at the single-cell level. Highlights and Figure/Table Index (Take-Home Messages)O_LIColon tissues from HD (n=4), patients with LS (n=6) and with CRC (n=3) were collected for snRNA-seq or scRNA-seq analysis; Diagnosis of the 6 LS patients are clearly supported by our pedigree documentations (Fig. 1 and Supp. Fig. 1) and briefed in Table 1; C_LIO_LIAmong the 6 patients with LS, 1 for snRNA-seq analysis (a carcinoma tissue only), 3 for scRNA-seq analysis (3 paired para-carcinoma and carcinoma tissues) and 3 for experimental validations; (Fig. 1) C_LIO_LIFollowing studies are focused on the comparisons between HD, LS and CRC; In addition, comparisons between paired carcinoma and para-carcinoma tissues from patients with LS were also performed; (Fig. 2-7) C_LIO_LIWhen HD and LS are compared, a cancer stem cell marker CEACAM5 is readily detected by snRNA-seq analysis; (Fig. 5) C_LIO_LIWhen carcinoma and para-carcinoma from LS patients are compared, increased immune cell infiltration of and enhanced DNA repair activity in the malignant tissues is readily detected by scRNA-seq analysis; in addition, three upregulated markers in LS carcinoma (BACE2, GRPC5A and OLFM4) were identified and validated by immunohistoinfloresnce; (Fig. 3 and Fig. 4) C_LIO_LISComatic algorithm-based mutation calling analysis suggests a comparable mutation burden between carcinoma and para-carcinoma from LS patients, but such mutation burdens are grossly greater than that from HD or that from patients with CRC; (Fig. 6) C_LI O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@174af7dorg.highwire.dtl.DTLVardef@1ad3e71org.highwire.dtl.DTLVardef@dea1e4org.highwire.dtl.DTLVardef@568f91_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1C_FLOATNO Enrollment of LS patients and overall design of the study. (A) Three family pedigrees of the LS patients (LS-CRC) who donated the samples for single-cell transcriptomic analysis. Cropped pedigree information is provided in the Main text. See the Supp. Fig. 1 for the complete pedigree information. (B) Two different platforms were used in the study: snRNA-seq and scRNA-seq. (C) Various types of comparison were performed to characterize the malignant transition of LS. C_FIG O_TBL View this table: org.highwire.dtl.DTLVardef@eb8e4eorg.highwire.dtl.DTLVardef@cbafaaorg.highwire.dtl.DTLVardef@79ca83org.highwire.dtl.DTLVardef@1de7544org.highwire.dtl.DTLVardef@1e4fcbc_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONClinical information of enrolled patients with LS. An Excel version of the table is provided in the Supp. Material C_TABLECAPTION C_TBL O_FIG O_LINKSMALLFIG WIDTH=160 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig2.gif" ALT="Figure 2"> View larger version (56K): org.highwire.dtl.DTLVardef@8cd71corg.highwire.dtl.DTLVardef@7e75b3org.highwire.dtl.DTLVardef@61757eorg.highwire.dtl.DTLVardef@68ca5f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 2C_FLOATNO snRNA-seq analysis of a frozen colon biopsy sample from a LS patient reveals a cluster of cancer stem cells (A) Frozen colon biopsy samples were subjected for snRNA analysis (Healthy donors, N=4; Lynch Syndrome, N=1) and epithelial cells were filtered out for further study. Data were integrated by the Seurat and Harmony standard procedure. Clusters 0-9 were identified in a total of 11,353 cells (the Healthy Controls have 7,373 cells; the LS patient has 3,980 cells). The malignancy of the epithelial cells was inferred by the inferCNV and SCEVAN algorithm (two major compartments: tumor and no-tumor). The portion of tumor or non-tumor cells in each cluster was also illustrated (right panel). Note that the major contributor in Cluster 4, 6, and 7 is the tumor-like cells from the LS patient. (B) Each cluster of the epithelial cells was further annotated according to the combination of Seurat cluster identity and SCEVAN malignant identity. Mix_1 to 5 contain both tumor-like cells and non-tumor-like cells; Other clusters are marked as BEST4+-Enterocytes, Enterocytes and Goblet cells where much fewer tumor-like cells were assigned. Note that the epithelial cells from the LS patient are mainly classified into Mix_2, 4, and 5 tumor-like cells. (C) Three clones were inferred by SCEVAN algorithm. In the phylogenetic tree, Clone_1 and Clone_2 are closer and probably originated from Clone_3. (D) A Sankey plot showing overall belonging relationships in the epithelial snRNA-seq dataset. Note that the Mix_2 pool is dominated by cells from Lynch_01 and that in the Mix_2 pool Clone_3 is the most dominant clone. (E) The Mix_2 cells specifically express numerous colon epithelial stem cells signature markers such as SMOC2, RGBM, OLFM4, AXIN2 and LGR5. Of note, all these intestine stem cell signature genes were reported as marker genes for cancer stem cells, especially LGR5. (F) Pseudotime trajectory analysis of the Lynch Syndrome epithelium cells indicates the Mix_2 cells are the most primitive in development. (G) Top 36 differentially expressed genes (DEGs, both upregulated and downregulated) were highlighted when the non-tumor-like cells were compared with tumor-like cells in the Mix2. (H) The Mix_2, 4, 5 epithelial cells all have enriched signaling pathways involved in DNA repair response and MYC targets (fonts in red) while Mix_4 and 5 manifest Interferon alpha or gamma response (fonts in blue). C_FIG O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig7.gif" ALT="Figure 7"> View larger version (54K): org.highwire.dtl.DTLVardef@1be2c6aorg.highwire.dtl.DTLVardef@55f267org.highwire.dtl.DTLVardef@9d60fborg.highwire.dtl.DTLVardef@4a2d37_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 7C_FLOATNO Distinct tumor immunity microenvironment profiles in LS carcinoma (A) T cells from LS-CA and LS-paraCA patients were filtered for further annotation. The LS-paraCA group had 1410 T cells, whereas the Lynch CA group had 2125 T cells. Six major T cell subtypes were identified: Naive CD4-T, NKT, Treg, IL7R+CD8_T, GZMA+CD8_T, and GZMK+CD8_T. Note that GZMA+CD8_T cells appear to be more abundant in Lynch CA (arrows). (B) The pseudotime trajectory indicating the T cells developed towards two branches: the Naive CD4-T and Treg branches, and GZMA+CD8_T and GZMK+CD8_T branches. GZMA+CD8_T cells appear to be more mature in LS-CA than in LS-paraCA (arrows). (C-F) Biological function-instructed scoring of the paired single-cell datasets of T cells from the three LS patients, including T cell cytotoxicity (B), T cell exhaustion (C), T cell immune escape (D), and T cell surveillance (E). (G) Circle plots showing interaction profiles across indicated cells in the paired LS samples. The direction of the lines indicates the direction of the cell-cell communication, the width of the lines indicates the interaction strength, and the color of the lines indicates the cell types of the senders. (H) Summary of the Study. In this study, we profiled Lynch Syndrome biopsy samples using single-cell or single-nucleus RNA-seq analysis. Paired carcinoma and adjacent para-carcinoma samples were included to facilitate the analysis, including tracing tumor clones, calculating mutation burden, identifying biomarkers for cancer stem cells, and tumor immune microenvironment changes during the transition from pre-carcinoma to carcinoma in the inheritable cancer Lynch Syndrome. See the text in the Discussion section for further detail. C_FIG O_FIG O_LINKSMALLFIG WIDTH=148 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig5.gif" ALT="Figure 5"> View larger version (44K): org.highwire.dtl.DTLVardef@1de7f42org.highwire.dtl.DTLVardef@74e8ddorg.highwire.dtl.DTLVardef@1642847org.highwire.dtl.DTLVardef@907a23_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 5C_FLOATNO Distinct pre-cancer signs in epithelial and immune cells of LS para-carcinoma (A) The scRNA-seq datasets of LS-paraCA were integrated with those of the colons from healthy donors (HD) (N=3, respectively; the HD group had 7885 cells in total, whereas the LS-paraCA group had 4766 cells). A dominance of CEACAM5high epithelial cells were identified in LS-paraCA. The sample from the patient with relapsed LS is marked with an arrow in the bar plot (left panel). (B) The portion of CEACAM5high epithelial cells, infiltrated CD8_T cells and macrophages was quantified. The sample from the relapsed LS patient is marked with arrows. (C, E) Top marker genes co-expressed in CEACAM5high epithelial cells and the enriched pathways are illustrated in the gene expression heatmap. Cells from the Enterocytes, Tufts, and Goblet subtypes were used as controls. (D, F) Quantification of the expression of CEACAM5 in epithelial cells of HD and LS-paraCA cells. C_FIG O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig3.gif" ALT="Figure 3"> View larger version (48K): org.highwire.dtl.DTLVardef@142c991org.highwire.dtl.DTLVardef@1bf5d99org.highwire.dtl.DTLVardef@99edd5org.highwire.dtl.DTLVardef@1cd5c15_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 3C_FLOATNO Distinct infiltration of immune cells in carcinoma and para-carcinoma tissues of LS (A) Fresh paired carcinoma (LS-CA) and adjacent para-carcinoma (LS-paraCA) biopsies of colon tissue was subjected to scRNA-seq analysis (N=3). Colorectal cancer (nonLS-CRC, they are not diagnosed as LS) tumor samples from the public dataset were also included as controls (N=4). Cells were first grossly annotated as stromal, epithelial, or immune cells. Note that the LS-CA group showed increased infiltration of myeloid cells compared with LS-paraCA group, but T cell infiltration was comparable between the two groups. (B) Expression of classic markers for annotating the major 5 cell types. (C) Detailed annotations of 16 cell types in paired LS-CA and LS-paraCA samples. (D) Stacked bar plot showing the contribution of sample sources in each cell type. (E) Quantification of immune cell infiltration in LS-CA compared with LS-paraCA. Although no significant differences were observed, the fold-changes were approximately 2-10. Although the overall T cell infiltration was comparable, infiltration of GZMA+CD8_T and GZMK+CD8_T cells appeared to be higher in LS-CA than in LS-paraCA. Of the three LS patients enrolled in the study, one was a relapsed patient (gray dashed line, surgery treatment performed; whose son donated the frozen sample in Figure 2), while the other two were treatment-naive (gray solid lines). (F) Boxplots show DNA repair score quantification per sample (above) or per epi-cell. (bottom). C_FIG O_FIG O_LINKSMALLFIG WIDTH=152 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig4.gif" ALT="Figure 4"> View larger version (51K): org.highwire.dtl.DTLVardef@1588458org.highwire.dtl.DTLVardef@58db3borg.highwire.dtl.DTLVardef@1a12084org.highwire.dtl.DTLVardef@15de70e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 4C_FLOATNO Prioritizing novel epithelial biomarkers for tracing the transition between para-carcinoma and carcinoma in LS (LS-paraCA vs. LS-CA) (A) Epithelial cells were filtered out for further analysis and annotated as clusters 0-9 in the UMAP plot. (B, C) Bar and pie plots show the contribution of sources to epithelial clusters. Cluster 0 contained cells largely from Lynch CA_02, whereas Cluster 9 was composed of Lynch paraCA_02. The patient who donated Lynch CA_02 and paraCA_02 is identified as a relapsed LS. (D) KEGG enrichment analysis showing the enriched bioprocesses in the four epithelial cell clusters. (E) Five genes with upregulated expression in LS carcinoma epithelial cells were prioritized based on the scRNA-seq and snRNA-seq datasets. (F) Expression of BACE2, GPRC5A and OLFM4 in the paired LS-paraCA and LS-CA groups. Epithelial cells are circled by dashed lines. Note that the expression of genes in epithelial cells from nonLS-CRC samples was also very strong. (G) Verification of the low-to-high transition in the expression of BACE2, GPRC5A and OLFM4. Paraffin sections from paired LS-paraCA and LS-CA samples were prepared, and immunohistochemical (IHF) staining was performed. The expression of the indicated proteins is labeled in green, whereas the nuclei are stained with DAPI in blue. In total, biopsy samples from 4 patients with LS were used for IHF verification. C_FIG O_FIG O_LINKSMALLFIG WIDTH=148 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig6.gif" ALT="Figure 6"> View larger version (28K): org.highwire.dtl.DTLVardef@1ec5210org.highwire.dtl.DTLVardef@1ffd6f9org.highwire.dtl.DTLVardef@17a7a8forg.highwire.dtl.DTLVardef@4819e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 6C_FLOATNO Increased mutation burden in the colon tissues from Lynch Syndrome (A) The schematic diagram for calculating mutation burden based on the scRNA-seq datasets using the SComatic algorithm. Only single-base substitutions (SBS) were called in this study. Once mutation calls were achieved, the mutation burden value was quantified by normalizing the total mutation calls to the total cell number in the samples or cell types (See Methods section for details). (B) The total SBS mutation burden in the four groups of samples was indicated. (C) The six different SBS mutation burdens in the four groups of samples as indicated. (D) The SBS mutation burden in the cell types of the four groups is indicated. Note that the The mutation burden appears to be higher in mast, epithelial, plasma, myeloid, and Treg cells in the LS-CA group than in that the LS-paraCA group. C_FIG

cancer biology↗

bioRxiv2025

Andrographolide prevents necroptosis by suppressing generation of reactive oxygen species

Andrographolide (Andro), a natural product extracted from the Chinese traditional medicine herb Andrographis paniculata, has been applied for the treatment of diverse inflammatory diseases. However, its effects on necroptosis, a lytic form of cell death implicated in various inflammatory diseases, remain uncharacterized. In the current research, we investigate whether Andro and its derivatives can suppress necroptosis. The results demonstrate that Andro notably inhibits the necroptosis in in vitro cellular models induced by either lipopolysaccharide (LPS) plus IDN-6556 or a combination of TNF-, LCL-161 (Smac mimetic) and IDN-6556. In these cellular models, Andro exhibits inhibitory effects on the phosphorylation of receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed lineage kinase domain-like protein (MLKL), as well as on the formation of necrosomes. Specifically, Andro reduces intracellular reactive oxygen species (ROS) and mitochondrial superoxide (mtROS), preserves mitochondrial membrane potential during necroptotic induction, and activates the antioxidant transcription factor nuclear factor E2-related factor 2 (Nrf2). Upon the necroptotic stimulation, some mitochondrial proteins such as Bcl-2 and Bak oligomerize and colocalize with RIPK1, RIPK3, and phosphorylated MLKL (p-MLKL) in necrosomes. However, such a process of necrosome formation can be prevented by Andro. In contrast, derivatives including dehydroandrographolide, neoandrographolide, 14-deoxy-11,12-didehydroandrographolide, and 14-deoxyandrographolide show no anti-necroptotic effects and fail to upregulate Nrf2. Collectively, our findings demonstrate that Andro specifically inhibits the RIPK1/RIPK3/MLKL signaling axis to suppress necroptosis, highlighting its therapeutic potential against necroptosis-related disorders.

pharmacology and toxicology↗

bioRxiv2025

TIR immune signaling is blocked by phosphorylation to maintain plant growth

Toll/interleukin-1 receptor (TIR) domain proteins are immune signaling components and function as NAD+-cleaving enzymes to activate defense responses. Activation of TIRs represses growth and drives cell death in plants and promotes axon degeneration in animals, but how plant TIRs are repressed remains unclear. Here, we show that TIR NADase activity requires a conserved serine residue spatially close to the catalytic glutamate. The plant Ca2+-dependent protein kinases (CPKs), the mammalian Ca2+/calmodulin-dependent protein kinase II delta (CAMK2D) and TANK binding kinase 1 (TBK1) phosphorylate TIR domains at this conserved serine, which blocks TIR NADase activities and functions and thus maintains growth in plants and suppresses SARM1 TIR signaling in animals, respectively. Our findings define a fundamental molecular mechanism by which phosphorylation at a conserved serine residue blocks TIR signaling to balance growth and defense trade-offs.

plant biology↗

bioRxiv2025

Spatial transcriptomics AI agent charts hPSC-pancreas maturation in vivo

Spatial transcriptomics has revolutionized our understanding of tissue organization by simultaneously capturing gene expression and spatial localization within intact tissues. However, analyzing these increasingly complex datasets requires specialized expertise across computational biology, statistics, and biological context. To address this challenge, we introduce the Spatial Transcriptomics AI Agent (STAgent), an autonomous multimodal agentic AI that integrates multimodal large language models (LLMs) with specialized computational tools to transform weeks-long analysis tasks into minutes of automated processing. Unlike conventional machine learning approaches that are limited to narrow, predefined tasks, STAgent leverages the emergent capabilities of multimodal LLMs - such as flexible reasoning, contextual understanding, and cross-modal integration - which allow it to adapt to novel data, execute multi-step analyses, and generate biologically meaningful insights with minimal human input. STAgent enables autonomous deep research through integrated capabilities, including dynamic code generation for complex analytical workflows, visual reasoning for interpreting spatial patterns, real-time retrieval of relevant peer-reviewd scientific literature, and synthesis of comprehensive, actionable reports. We applied STAgent to investigate the in vivo maturation of human stem cell-derived pancreatic cells (SC-pancreas) transplanted into immunodeficient mice. We generated single-cell spatial transcriptomics data spanning multiple developmental timepoints. STAgent autonomously (1) identified the maturation of initially scattered endocrine cells into well-defined islet-like structures, with predominantly peripheral -cells surrounding {beta}-cell cores supported by an expanding mesenchymal network; (2) revealed strengthening endocrine-endocrine cell interactions over time and, through context-aware gene set analysis, uncovered spatially resolved biological processes driving maturation; (3) unlike traditional analytical approaches, STAgent offers mechanistic explanations of spatial patterns, contextualizing findings with relevant literatures and developing cohesive insights into human pancreatic development. This agentic approach establishes a new paradigm in spatial transcriptomics analysis by substantially lowering the expertise barrier and reducing analysis time, accelerating biological and biomedical discovery.

genomics↗

bioRxiv2025

In Situ Graphene-Seq: Spatial Transcriptomics and Chronic Electrophysiological Characterization of Tissue Microenvironments

Biological systems are composed of diverse, interconnected cell types, yet capturing both their functional dynamics and molecular identities at high spatiotemporal resolution remains challenging. While electrophysiological measurements provide real-time insights into cellular activities, they cannot fully describe the molecular architecture and states of the measured cells. Conversely, transcriptomics reveals cell gene expression patterns but does not capture functional states. Bridging these modalities is essential for a holistic understanding of the molecular mechanisms driving functional changes. In this study, we introduce in situ graphene-sequencing (graphene-seq), a unique platform that seamlessly integrates chronic electrophysiology with imaging-based, spatially resolved 3D transcriptomics, overcoming longstanding limitations of current multimodal approaches. This system leverages stretchable mesh nanoelectronics for long-term, single-cell-level interfacing and incorporates transparent graphene/PEDOT:PSS electrodes, enabling seamless integration of electrical recordings and optical imaging. By combining electrophysiology with high-throughput, imaging-based in situ sequencing, this platform allows comprehensive multimodal, spatially resolved analysis of cell microenvironment within spatially heterogeneous tissues. We validate in situ graphene-seq by charting multimodal profiles of human-induced pluripotent stem cell-derived cardiomyocyte and endothelial cell co-cultures, examining how spatial heterogeneity in cell composition influences both electrophysiological activity and gene expression. This scalable, integrated approach offers a powerful tool for studying the complex interplay between cellular function and molecular identity. It also provides insights into how tissue microenvironments shape cell behavior and molecular states, advancing applications in regenerative medicine, stem cell therapy, and disease modeling.

bioengineering↗

bioRxiv2025

Munc13-4 mediates tumor immune evasion by regulating the sorting and secretion of PD-L1 via exosomes

Tumor-derived extracellular vesicles primarily carry PD-L1 via exosomes, which interact with PD-1 receptors on T cells, impacting immune responses in the tumor microenvironment and beyond, leading to a more extensive immunosuppressive landscape. However, the mechanisms governing exosomal PD-L1 sorting and secretion remain elusive. In this study, we identified Munc13-4 as a crucial regulator of exosomal PD-L1 sorting and secretion. Deletion of Munc13-4 in breast tumors enhances T cell-mediated anti-tumor immunity, suppresses tumor growth, and improves the efficacy of immune checkpoint inhibitors. Our results illustrate how Munc13-4 collaborates with HRS, Rab27, and SNAREs to facilitate PD-L1 sorting and secretion via exosomes. The cryo-EM structure of the Munc13-4-Rab27a complex provide new insights into its role in exosome secretion. Importantly, we discovered that Munc13-4 has a novel role in sorting PD-L1 onto exosomes, which relies on the formation of a ternary complex with PD-L1 and HRS. In addition, IFN{gamma} stimulation modifies Munc13-4 and HRS, establishing a dynamic regulatory mechanism that enables tumor cells to adapt to immune pressure by modulating PD-L1 sorting. Using a specially designed peptide to disrupt the Munc13-4-PD-L1 interaction and impede PD-L1 sorting significantly enhances anti-tumor immunity and slows tumor growth in vivo. These results highlight the potential of targeting the Munc13-4-PD-L1 axis to suppress tumor immune evasion.

cell biology↗

bioRxiv2025

Chemoselective Characterization of New Extracellular Matrix Deposition in Bioengineered Tumor Tissues

The extracellular matrix (ECM), present in nearly all tissues, provides extensive support to resident cells through structural, biomechanical, and biochemical means, and in return the ECM undergoes constant remodeling from interacting cells to adapt to the evolving tissue states. Bioengineered 3D tissues, commonly known as cell-ECM composites, are robust model systems to recapitulate and investigate native pathophysiology. Key to this engineered morphogenesis process are the intricate cell-ECM interactions reflected by how cells respond to and thereby modulate their surrounding microenvironments through their ongoing ECM secretome. However, investigating ECM-regulated new ECM production has been challenging due to the proteomic background from the pre-existing biomaterial ECM. To address this hindrance, here we present a chemoselective strategy to label, enrich, and characterize newly synthesized ECM (newsECM) proteins produced by resident cells, allowing distinction from the pre-existing ECM background. Applying our analytical pipeline to bioengineered tumor tissues, either built upon decellularized ECM (dECM-tumors) or as ECM-free tumor spheroids (tumoroids), we observed distinct ECM synthesis patterns that were linked to their extracellular environments. Tumor cells responded to the dECM presence with elevated ECM remodeling activities, mediated by augmented digestion of pre-existing ECM coupled with upregulated synthesis of tumor-associated ECM. Our findings highlight the sensitivity of newsECM profiling to capture remodeling events that are otherwise under-represented by bulk proteomics and underscore the significance of dECM support for enabling native-like tumor cell behaviors. We anticipate the described newsECM analytical pipeline to be broadly applicable to other tissue-engineered systems to probe ECM-regulated ECM synthesis and remodeling, both fundamental aspects of cell-ECM crosstalk in engineered tissue morphogenesis.

bioengineering↗

bioRxiv2025

Beyond Pairwise Connections in Complex Systems: Insights into the Human Multiscale Psychotic Brain

Complex biological systems, like the brain, exhibit intricate multiway and multiscale interactions that drive emergent behaviors. In psychiatry, neural processes extend beyond pairwise connectivity, involving higher-order interactions critical for understanding mental disorders. Conventional brain network studies focus on pairwise links, offering insights into basic connectivity but failing to capture the complexity of neural dysfunction in psychiatric conditions. This study aims to bridge this gap by applying a matrix-based entropy functional to estimate total correlation, a mathematical framework that incorporates multivariate information measures extending beyond pairwise interactions. We apply this framework to fMRI-ICA-derived multiscale brain networks, enabling the investigation of interactions beyond pairwise relationships in the human multiscale brain. Additionally, this approach holds promise for psychiatric studies, providing a new lens through which to explore beyond pairwise brain network interactions. By examining both triple interactions and the latent factors underlying the triadic relationships among intrinsic brain connectivity networks through tensor decomposition, our study presents a novel approach to understanding higher-order brain dynamics. This framework not only enhances our understanding of complex brain functions but also offers new opportunities for investigating pathophysiology, potentially informing more targeted diagnostic and therapeutic strategies. Moreover, the methodology of analyzing multiway interactions beyond pairwise connections can be applied to any signal analysis. In this study, we specifically explore its application to neural signals, demonstrating its power in uncovering complex multiway interaction patterns of brain activity, which provide a window to explore connectivity beyond pairwise interactions in the multiscale functionality of the brain.

neuroscience↗

bioRxiv2025

Fecal microbiota transplantation mitigates cardiac remodeling and functional impairment in mice with chronic colitis

BackgroundInflammatory bowel disease (IBD) is a chronic inflammatory disorder with significant extraintestinal manifestations, including cardiovascular derangements. However, the molecular mechanisms underlying the cardiac remodeling and dysfunction remain unclear. MethodsWe investigated the effects of chronic colitis on the heart using two mouse models: DSS-induced colitis and Il10-/-spontaneous colitis. Echocardiography was employed to assess heart function and molecular characterization was performed using bulk RNA-sequencing, RT-qPCR, and western blot. ResultsBoth models exhibited significant cardiac impairment, including reduced ejection fraction and fractional shortening as well as increased collagen deposition, inflammation, and myofibril reorganization. Molecular analyses revealed upregulation of fibrosis markers (i.e. COL1A1, COL3A1, Fibronectin) and {beta}-catenin reactivation, indicating a pro-fibrotic cardiac environment. Each model yielded common upregulation of eicosanoid-associated and inflammatory genes (Cyp2e1, Map3k6, Pck1, Cfd), and model-specific alterations in pathways regulating cAMP- and cGMP-signaling, arachidonic and linoleic acid metabolism, Cushing syndrome-related genes, and immune cell responses. DSS colitis caused differential regulation of 232 cardiac genes, while Il10-/- colitis yielded 105 dysregulated genes, revealing distinct molecular pathways driving cardiac dysfunction. Importantly, therapeutic fecal microbiota transplantation (FMT) restored heart function in both models, characterized by reduced fibrosis markers and downregulated pro-inflammatory genes (Lbp and Cdkn1a in Il10-/- mice and Fos in DSS mice), while also mitigating intestinal inflammation. Post-FMT cardiac RNA-sequencing revealed significant gene expression changes, with three altered genes in DSS mice and 67 genes in Il10-/- mice. Notably, Il10-/- mice showed relatively less cardiac recovery following FMT, highlighting IL-10s cardioprotective and anti-inflammatory contribution. ConclusionsOur findings elucidate novel insights into colitis-induced cardiac remodeling and dysfunction and suggest that FMT mitigates cardiac dysfunction by attenuating systemic inflammation and correcting gut dysbiosis. This study underscores the need for further evaluation of gut-heart interactions and microbiome-based therapies to improve cardiovascular health in IBD patients. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/643179v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@13d79eaorg.highwire.dtl.DTLVardef@10f28a7org.highwire.dtl.DTLVardef@35f4b0org.highwire.dtl.DTLVardef@538d7e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Spatial relationship of urban carbon neutrality in Yangtze River Basin

Carbon neutrality needs to be implemented spatially in order to be realized concretely. The distribution of carbon sources and sinks across the national territory is closely related to many factors, such as natural geographical resources, levels of economic and social development, and cultural and historical heritage. It is difficult for many regions to achieve carbon neutrality through their own efforts alone. This article believes that only by achieving local optimal carbon neutrality through a reasonable spatial organization can emissions be ultimately reduced to zero on a national scale. Under the connection of rivers, the basin forms an ecosystem and an economic system with independent characteristics. Carbon sources and sinks within the basin exist within the ecological and economic space of the basin, forming a unique carbon neutrality spatial pattern. This study starts with the spatial distribution status, features and relationships of carbon neutrality elements in the cities of the Yangtze River Basin, and divides the cities into eight types based on their development level, emission level and forest resources, such as high-emission and low-carbon sink developed cities and low-emission and high-carbon sink underdeveloped cities. Different types of cities are proposed with carbon neutrality paths and spatial organization schemes, and it is suggested that the spatial organization demonstration of carbon neutrality in the cities of the Yangtze River Basin can provide a reference for carbon neutrality on a national scale.

ecology↗

bioRxiv2025

Lamin A/C safeguards replication initiation by orchestrating chromatin accessibility and PCNA recruitment

Lamin A/C, a nuclear lamina protein, is essential for maintaining nuclear architecture, organizing chromatin and preserving genomic stability. However, its role in regulating DNA replication remains unclear. This study investigates how Lamin A/C regulates proper activation of replication origins by orchestrating the chromatin structure and recruitment of proliferating cell nuclear antigen (PCNA). We demonstrate that Lamin A/C stabilizes replication domains (RDs) by restricting chromatin mobility, preserving spatial organization, and maintaining accessibility. Furthermore, Lamin A/C interacts with PCNA and sequesters a pool of PCNA, to regulate its recruitment to replication machinery. The loss of Lamin A/C leads to an increase in chromatin dynamics, RD accessibility, and PCNA availability at RDs, which together trigger excessive activation of replication origins, leading to replication stress and DNA damage. These disruptions prolong the S phase and compromise genome stability, highlighting Lamin A/C as a critical gatekeeper of balanced replication initiation. Our findings reveal Lamin A/Cs dual role in chromatin organization and replication machinery regulation, offering valuable insights into its involvement in replication-associated diseases and potential therapeutic opportunities through targeting replication dynamics.

biophysics↗

bioRxiv2025

De novo Genome Assembly and Annotation of Manouria impressa

The Manouria impressa (Impressed tortoise) is a unique fungivore species with restricted distribution in Southeast Asia, recognized for its evolutionary importance and conservation priority. Here, we present the first de novo genome assembly of an impressed tortoise sampled from Yunnan, China. Using PacBio HiFi long-read sequencing and Hi-C proximity ligation technologies, we generated a 2.29 Gb assembly comprising 81 scaffolds with a contig N50 of 78.37 Mb, a scaffold N50 of 148.31 Mb, and a BUSCO completeness score of 98.3%. This high-quality genome assembly provides a critical resource for exploring the genetic basis of evolutionary adaptations and informing conservation genomics to support the management of this vulnerable species.

genomics↗

bioRxiv2025

Alternate isoforms of IRF7 Differentially Regulate Interferon Expression to Tune Response to Viral Infection

Interferon Regulatory Factor 7 (IRF7), and its homologue IRF3, are master transcriptional regulators of the innate immune response. IRF7 binds to promoters of interferon {beta} (IFN{beta}) and several IFNs as a homodimer or as a heterodimer with IRF3 to drive expression of these type I IFNs, which in turn activate downstream signaling pathways to promote expression of antiviral genes. Here we demonstrate that alternative splicing of the first intron within the coding region of IRF7 is highly regulated across immune tissues and in response to immunologic signals including viral infection. Retention of this intron generates an alternative translation start site, resulting in a N-terminally extended form of the protein (exIRF7) with distinct function from the canonical version of IRF7 (cIRF7). We find that exIRF7 uniquely activates a gene expression program, including IFN{beta}, in response to innate immune triggers. Mechanistically, this enhanced activity of exIRF7 relative to cIRF7 is through increased homodimerization and association with IRF3 on DNA. Furthermore, the enhanced transcriptional activity of exIRF7 controls viral infection to a greater extent than cIRF7, demonstrating that alternative splicing of IRF7 is a previously unrecognized mechanism used by cells to tune the interferon response to control viral infections and other immune challenges. HighlightsO_LIIntron retention in the human IRF7 gene generates a distinct protein isoform that differs in the N-terminus. C_LIO_LIIRF7 intron retention is regulated in a stimuli- and cell-type specific manner. C_LIO_LIThe extended version of IRF7, produced by intron retention, exhibits enhanced transcriptional activation of type I interferon genes. C_LIO_LICells expressing the extended version of IRF7 are more resistant to viral infection. C_LI

molecular biology↗

bioRxiv2025

Transcriptomic splicing analysis reveals a gene-independent form of TE reactivation in tumors representing unrecognized source of oncogenes and neoantigens

Transposable elements (TEs) are reactivated in tumors and serve as significant contributors to tumor transcriptomic complexity and heterogeneity. However, their repetitive nature and diverse transcriptional forms have hindered efforts to characterize TE-derived transcripts independent of host gene contexts. Here, using our self-developed splicing-junction analysis tool ASJA, we systematically interrogated TE transcription across 32 cancer types, identifying transcripts autonomously initiated from and exclusively spliced among TEs with high TE content, termed TEtrans. Our analysis revealed 5,361 TEtrans exhibiting pan-cancer prevalence, tumor-specific expression and features of mature transcripts, including canonical splicing, 5 caps and polyA tails. Mostly unannotated and enriched in intergenic regions, TEtrans are predominantly derived from primate-specific classes with conserved splice pattern. TEtrans burden demonstrates heterogeneous associations with prognosis and immune activity across cancers, while their expression can be epigenetically dual-regulated by stemness- and inflammation-associated transcription factors. Functional studies uncovered that TEtrans could act as oncogenes, exemplified by tsTE1, a HERVH-derived transcript that promotes colorectal cancer proliferation by enhancing TOP1-mediated DNA supercoil relaxation. Remarkably, [~]7.2% of TEtrans are identified to encode tumor neoantigens, including viral proteins and unannotated peptides, which are shared among patients and validated by proteogenomic analysis. These TEtrans-derived neoantigens are immunogenic both in vitro and in vivo, and exceed neoepitopes from genomic alterations in abundance per tumor, particularly in cancers with low mutational burden. Collectively, as a gene-independent form of TE-derived transcripts, TEtrans represents a unique source of oncogenes and tumor neoantigens, expanding the functional repertoire of TEs in cancer biology and offering new avenues for therapeutic targeting. HighlightsO_LITEtrans are tumor-specific transcripts with conserved splicing patterns, predominantly derived from primate TEs in intergenic regions. C_LIO_LITEtrans expression is epigenetically activated and dually regulated by stemness/inflammation transcription factors. C_LIO_LITEtrans function as oncogenes, exemplified by tsTE1 enhancing TOP1-mediated DNA relaxation. C_LIO_LITEtrans encode tumor neoantigens that elicit CD8+ T cell responses, providing targets for immunotherapy, especially in low-mutation tumors. C_LI Abstract figure O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/640928v1_ufig1.gif" ALT="Figure 1"> View larger version (78K): org.highwire.dtl.DTLVardef@1d2d4cforg.highwire.dtl.DTLVardef@918f14org.highwire.dtl.DTLVardef@489465org.highwire.dtl.DTLVardef@1069d17_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Endurance Exercise Ameliorates Aging-Related Bradyarrhythmia in Drosophila Resulting from miR-283 Knockdown in LNvs

MicroRNAs (miRNAs) are crucial in regulating cardiac aging and related diseases, yet few functional miRNAs have been identified. Prior studies showed miR-216a upregulation in heart failure patients, but its impact on aging hearts is unknown. Our study revealed systemic miR-283 overexpression or knockdown caused age-related bradycardia, mimicking human bradyarrhythmia. Importantly, we found that knockdown of miR-283 in ventral-lateral neurons (LNvs), rather than in the heart, led to the occurrence of bradyarrhythmia, which was mainly caused by the upregulation of miR-283 expression in the whole brain and heart. The gene of clockwork orange (cwo) may mediate miR-283s effect on heart rhythm. Additionally, to investigate the miRNA regulatory mechanism underlying exercise-induced delay in cardiac aging, we conducted a three-week endurance exercise program on miR-283 knockdown flies in LNvs. We found that exercise significantly downregulated the accumulation of miR-283 in the brain and myocardium caused by aging or miR-283 knockdown in LNvs, improved the structure of myocardial fibers, and effectively reduced bradyarrhythmia. Our findings provides a new perspective on distal neuromodulation and intervention in cardiac aging.

physiology↗

bioRxiv2025

Synergistic neuroprotective and cognitive-enhancing effects of Walnut Peptide and Theanine in human brain organoid and mouse stress models

Stress is a prevalent mental health concern emerging predominantly in late adolescence or early adulthood. Since 2007, the Food and Drug Administration (FDA) has not approved any novel anxiolytic pharmaceuticals, fueling interest in nutritional supplements as alternative therapies for stress management. Building on prior zebrafish research, this study investigates the synergistic effects of Theanine (Th) and Walnut Peptide (WP) on stress mitigation and cognitive enhancement. Utilizing the human brain organoid stress (BO-stress) model, WP+ Th were observed to reduce stress and regulate expression of neurotransmitters, including Gamma-Aminobutyric Acid (GABA), serotonin (5-HT), dopamine (DA), and acetylcholine (Ach), as well as brain-derived neurotrophic factor (BDNF) and serotonin transporter (SERT). Subsequent in vivo study using C57BL/6J mouse-stress model demonstrated that the treatment (Th 85 mg/mL + WP 200 mg/mL), or administrated with vehicles, significantly improved their performance in stress and cognitive assessments, partially normalized neurotransmitter imbalances by modulating SERT and BDNF expression. These findings highlighted the potential of using WP + Th, particularly when delivered with vehicles (eg: powder/yogurt/milk), as a novel combined therapeutic approach for stress management and cognitive enhancement. We performed a correlation analysis between BO-stress model and mouse-stress model, revealing a alignement in the SERT levels.In addition, SERT was highly correlated with other markers in the mouse hippocampus and may represent a key target for modulating the balance between stress and cognition. Significance StatementThis study established an innovative human brain organoid-stress model and, in conjunction with mouse-stress model, elucidated the synergistic actions of Theanine and Walnut Peptide in mitigating stress and augmenting cognitive function. Their beneficial effects were mediated through the regulation of SERT and BDNF, presenting a promising non-pharmacological avenue for mental health care. In addition, species differences between humans and mice were also examined through correlation analysis of brain organoids and mouse models. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/640260v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@1a81886org.highwire.dtl.DTLVardef@e2281dorg.highwire.dtl.DTLVardef@1b7b167org.highwire.dtl.DTLVardef@dff9aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

Genome-wide profiling of tRNA modifications reveal the presence of divergent signatures in Plasmodium falciparum

tRNAs are known to be extensively decorated with various nucleotide modifications, which can modulate the biological properties of tRNAs, such as promoting translation efficiency or fidelity, influencing codon preference and stabilizing tertiary structure of tRNAs. Dynamic alteration of the tRNA modifications, particularly under stress, are conserved gene regulatory mechanisms employed by cells across the kingdoms of life. The malaria-causing Plasmodium falciparum, which has a highly AT-biased genome, is reliant on a non-redundant set of tRNA genes to decode distinct and codon-skewed transcriptomes across its developmental stages. This genomic feature highlights the regulatory potential of tRNA modifications and warrants studies on how the tRNA epitranscriptome can impact gene regulatory function in this parasite. However, systematic studies of tRNA modifications in P. falciparum remain sporadic. In this study, we present a sequencing-based analysis of tRNA modifications in P. falciparum through optimizing the TGIRT-tRNA sequencing approach. The optimized protocol significantly reduces reverse transcription (RT) stop-induced short reads and enhances full-length cDNA synthesis, enabling the identification and stoichiometric estimation of a select nucleotide modifications at single-base resolution. We were able to identify seven types of conserved tRNA modifications and discovered two non-canonical signatures at A59 and U73 positions on specific nuclear-encoded tRNAs, which provides new insights into previously unreported modification sites. Our findings further reveal the dynamic nature of tRNA modifications during stage progression and under stress conditions.

microbiology↗