Biology subjects

Liu, L.

Publications and source records attributed to Liu, L..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

Effective repurposed antivirals against an emerging virus

The ongoing global monkeypox virus (MPXV) outbreak urgently needs effective medications, which be accelerated through drug repurposing. However, it is challenging to poinpoint protein targets. Here we introduce a novel method rooted in molecular evolutionary theory for quick drug target identification for MPXV. It identifies drug targets as positively selected genes of viral proteins which bind host proteins. From the identified targets, we select a top gene product OPG021 for virtural drug screening. One top-ranked drug nilotinib is experimentally shown to have a significant 69% of antiviral efficacy of the FDA-approved antiviral tecovirimat (TPOXX(R) or ST-246). Higher binding affinity but not antiviral efficacy of repursposed drugs than FDA-approved drugs suggests the complexity of drug repurposing and underscores the importance of experimental validation. This innovative drug target identification strategy will contribute to combating the ongoing MPXV outbreak and other viral acute and chronic viral diseases.

pathology↗

bioRxiv2025

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

bioRxiv2025

Discovering Condition-specific Cell Populations via Integrative Clustering of Single-cell Data

We present INtegrative CLustering Of Single cElls (INCLOSE), a novel computational method that integrates single-cell omics data and sample metadata to identify cell populations. INCLOSE analysis of CITE-seq data of acute myeloid leukemia and healthy samples uncovered cell populations exclusively found in the leukemia samples or the healthy samples. These condition-specific cell populations strongly suggested that immune suppression in tumor microenvironment plays a pivotal role in driving tumor progression.

bioinformatics↗

bioRxiv2025

ceQTL: A co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation

Expression quantitative trait locus (eQTL) mapping is used to identify a functional link between a genomic variant, such as single nucleotide polymorphism (SNP), and gene expression (often close-by pair for cis-eQTL) by linear regression, commonly done when matching genotype and expression data from same individuals are available. Millions of significant eQTLs have been reported by both individual studies and coordinated large consortiums such as Genotype-Tissue Expression project (GTEx). A significant eQTL association does not establish a causal relationship or provide any underlying mechanism so further investigation is needed to understand how a SNP impacts gene expression. One of the plausible explanations for eQTL is that a genomic variant affects transcription factor (TF) binding and thus impacts its regulation on its target genes (TGs). However, data-driven or formal statistical methods to prove that hypothesis are still lacking. To address the gap, we propose a new method called differential co-expression QTL (ceQTL) among different alleles using Chow statistics to specifically detect eQTLs that are modulated by a particular TF. We start with building a trio of TF, its TG, and related SNP and then test the significant coefficient difference among different levels of SNP in terms of TF and TG correlation. We applied this ceQTL model to simulated data and the lung tissue datasets from the GTEx project. The simulated data results showed that the model was robust to detect true ceQTLs at variable sample sizes and different minor allele frequencies as measured by Area Under the Curve (AUC). In normal lung tissue, a small fraction of eQTLs were found to have strong ceQTLs, i.e., eQTLs where SNP affects gene expression though TF binding. Some ceQTLs may not be detected by traditional eQTL analysis. Our tool also performed a TF binding affinity analysis to add another layer of evidence for functional interpretation. Comparisons with other similar tools were also presented. In summary, ceQTL analysis provides a more interpretable and biological insight into the mechanism of eQTL, which would help us better understand how genomic variants affect phenotypes and diseases.

bioinformatics↗

bioRxiv2025

Inducing TRIB2 Targeted Protein Degradation to Reverse Chemoresistance in Acute Myeloid Leukemia

The myeloid oncogene TRIB2 is a key driver of acute myeloid leukaemia (AML) pathogenesis, promoting chemoresistance and blocking differentiation through ubiquitin-mediated degradation of the C/EBP transcription factor. Despite its stable and sometimes elevated expression across AML subtypes, TRIB2 remains a clinically-untargeted vulnerability. Here, we present a comprehensive investigation into TRIB2 degradation mechanisms using multimodal approaches, including CRISPR knockout, mutational protein stability, small molecule TRIB2 engagement and evaluation of a novel targeted protein degrader (TRIB2-PROTAC). We identify Afatinib, a multi-ERBB covalent inhibitor, as a rapid inducer of TRIB2 degradation, triggering AML cell death via an ERBB-independent pathway. Importantly, TRIB2 degradation synergized with cytarabine, the frontline AML chemotherapy, amplifying therapeutic efficacy. Mapping of TRIB2 ubiquitination sites revealed Lys-63 as critical for its own proteolytic turnover, and a Lys to Arg degradation-resistant mutant (KallR) conferred enhanced chemoresistance and increased leukaemic engraftment in vivo. CRISPR-mediated TRIB2 knockout validated an essential role in AML cell survival. Consistently, the novel TRIB2-PROTAC (compound 5K) achieved robust TRIB2 degradation and AML cell killing at low micromolar concentrations. These findings establish TRIB2 as a compelling therapeutic target in AML and demonstrate that leveraging the ubiquitin-proteasome system to degrade TRIB2 offers a promising strategy to overcome chemoresistance. This work provides strong preclinical rationale for the development of TRIB2-targeting therapies in AML.

cancer biology↗

bioRxiv2025

Common-specific edge-centric connectome across Four Episodes in Bipolar Disorder

BackgroundBipolar disorder (BD) is a heterogeneous psychiatric illness marked by dynamic mood states, including manic (BipM), depressive (BipD), mixed (mBD), and euthymic/remitted (rBD) episodes. These clinical fluctuations are accompanied by widespread functional disruptions in the brain. However, the shared and individual-specific neural mechanisms across distinct episodes of BD remain poorly understood. MethodsWe analyzed resting-state fMRI data from 190 participants (BD patients in four episodes and healthy controls) using edge-centric functional connectomes (eFC), which capture time-resolved co-fluctuations between brain regions. A common-orthogonal-basis extraction (COBE) algorithm was applied to decompose individual eFC matrices into shared and individual-specific subspaces. We characterized the spatial topology, genetic relevance, and circuit-level correlates of the shared component. Dynamic properties (entropy, identifiability) and symptom prediction models were assessed using entropy metrics, intraclass correlation coefficients, and support vector regression. ResultsThe shared eFC pattern was stable across participants, aligned with the sensory-association gradient (p < 0.0001), and exhibited significant heritability and test-retest reliability (p < 0.05). Entropy of individual loadings increased with illness duration and was significantly elevated in BD, particularly in mBD. Microcircuit modeling revealed that this shared pattern was inversely related to external input strength (r = - 0.34, pspin< 0.05), indicating intrinsic network dominance. mBD was associated with globally elevated eFC entropy and markedly reduced fingerprint stability. Symptom severity (HDRS, YMRS, HAMA) was significantly predicted from individual network topographies across BD phases, highlighting clinically meaningful dynamic signatures. ConclusionOur findings demonstrate that BD episodes are underpinned by a conserved functional scaffold and distinct individual-specific neural fingerprints. Edge-centric dynamics--especially those derived from individual-specific decompositions--offer robust biomarkers for mood state characterization and symptom severity, and may facilitate future personalized interventions in BD.

neuroscience↗

bioRxiv2025

XomicsDB: a database of paired multi-omics datasets for systems biology

Life science research is primarily driven by data integration on the basis of theoretical development. Broad applications of multiomics (xomics) data calls for efficient integration of xomics data to infer cellular operation and regulation. To that end, it is urgently needed good-quality xomics data should be curated and shared for the community. Here we present XomicsDB, a database curating paired xomics datasets at both bulk and single-cell levels in model organisms. It contains 183 datasets from 13 model organisms, with a total of seven xomics data types. Users can download these datasets individually or in a batch from the ftp server provided. Users can also upload their paired xomics datasets for sharing. Incoporation of xomics data intom GSMs are demonstrated in model organisms Escherichia coli and human. Future efforts will be on collecting more single-cell xomics data and curating non-model oragnisms. The XomicsDB can be found at: http://xomicsdb.com.

systems biology↗

bioRxiv2025

Fluorescently Labeled Gradient Hydrogels Reveal Matrix-Dependent Cell Responses to Substrate Stiffness

Microfabricated stiffness gradient hydrogels hold significant value for advancing mechanobiology, tissue engineering, and in vitro tissue models. However, it remains challenging to design these materials given their broad processing parameter space. The continuum of stiffness values also makes it difficult to precisely correlate the local substrate properties and observed biological responses, often relying on cumbersome characterization methods such as atomic force microscopy. To address these bottlenecks, we present a straightforward thermophoresis-based fabrication strategy to pattern stiffness gradients in fluorescein isothiocyanate-labeled hydrogel network, which displays a polymer concentration-dependent fluorescence readout. This approach enables quantitative assessment of the gradient formation process and contactless stiffness mapping via standard microscopy imaging. Using gelatin methacryloyl and Gellan gum as model systems, it is shown that substrate stiffness and extracellular matrix protein composition work together to affect 3T3-L1 fibroblast cell morphology and migration, with the underlying hydrogel type also affecting the outcome. By offering a simple and reliable approach for characterizing stiffness gradient hydrogels, this work advances the thermophoretic fabrication platform, opening avenues for new biomaterial systems for understanding and controlling the cell-material interplay.

bioengineering↗

bioRxiv2025

The anti-virus T cell response dominates the anti-cancer response in oncolytic virus therapy

Oncolytic viruses have strong potential as immunotherapies. By causing cancer cells to die and relieve antigens, these viruses can stimulate robust, systemic immune responses that may eliminate disseminated disease and prevent recurrence. Unfortunately, clinical trials using oncolytic viruses have not induced clearance of metastasis or protection from recurrence. Likewise, the combination of the only FDA-approved oncolytic virus-- Talimogene laherparapvec--with immune checkpoint blockade did not improve progression-free or overall survival. Because of these disappointing clinical trials, we sought to measure the ability of oncolytic viruses to induce cancer antigen presentation and the elicitation of cancer antigen-specific immune responses. Our data revealed that despite improved antigen presentation by dendritic cells, priming of cancer antigen-specific T cells was limited. However, viral antigen-specific T cells did develop and were in a phenotypic state to induce an effective response against virally infected cells. These preclinical results were mirrored in human peripheral blood samples. Overall, these data show that oncolytic virus treatment induces a response against the virus itself, but not cancer antigen, explaining the lack of response in metastatic disease. These interesting findings identify a critical mechanism that needs to be overcome to increase the efficacy of oncolytic virus therapy.

immunology↗

bioRxiv2025

Water body size shapes body size evolution via subgenomic selection in allopolyploid fish

Allopolyploidization is a major force in species evolution, and studying allopolyploids in diverse environments provides insights into their genetic mechanisms. Here, we investigated how water body size variation influences body size in allopolyploid fish. We used a nascent allopolyploid lineage derived from goldfish (Carassius auratus) and common carp (Cyprinus carpio) and established two populations in small and large water bodies for two generations. Genomic, transcriptomic, and epigenomic analyses revealed that the larger population had higher genetic diversity in subgenome R, while the smaller population had higher diversity in subgenome C. Potential selection regions were associated with growth regulatory genes, suggesting a role for gene regulation in body size adaptation. Dynamic gene expression patterns in various tissues indicated potential mechanisms underlying muscle development and adaptation to smaller water bodies. Furthermore, selection regions were linked to changes in chromatin accessibility, with subgenome R being more susceptible to these changes during genetic divergence. Our findings demonstrate that water body size variation drives body size in allopolyploid fish through subgenomic selection, impacting genetic variation, gene regulation, and epigenetic mechanisms.

genomics↗

bioRxiv2025

Overcoming impaired antigen presentation in tumor draining lymph nodes facilitates immunotherapy

Immunotherapies have revolutionized cancer care in recent decades, but approved therapies often fail and currently only target specific steps in the generation of anti-cancer immune responses. Notably, the majority of approved immunotherapies do not target antigen processing and presentation, which are key steps in the development of immune responses and harbor potential as targets to improve immunotherapy. Here, we demonstrate that breast tumors induce locoregional lymph node impairment in antigen presentation--but not in antigen processing--which limits anti-cancer antigen- specific T cell responses. Inhibition of the locoregional T cell response was due to a tumor-mediated reduction of the cytokine IL1{beta} in tumor draining lymph nodes, which impaired antigen presentation. Further, we tested the ability of dendritic cells in lymph nodes at various distances from the primary tumor to be activated utilizing an antigen- agnostic adjuvant delivery strategy. We observed improved anti-tumor T cell responses when the adjuvant was delivered to cancer antigen-positive lymph nodes distant from the tumor, suggesting these lymph nodes can be targeted to improve anti-cancer immune responses. When combined with immune checkpoint blockade, delivery of the adjuvant to distant lymph nodes led to long-term survival and protection from recurrence. Antigen presentation and T cell responses could also be recovered by exogenous delivery of IL1{beta} via intratumoral injection, with improved survival when combined with immune checkpoint blockade. Our study demonstrates that tumor- induced locoregional impairment of antigen presentation can be overcome by the appropriate introduction of immunological adjuvant to tumor-distant lymph nodes or by restoring IL1{beta} to the tumor-draining lymph node. These strategies can induce high- quality, durable immune responses and have clinical implications for expanding the efficacy of immunotherapies. SummaryBreast tumors induce locoregional lymph node impairments in antigen presentation, which can be remedied via either IL1{beta} delivery or antigen-agnostic adjuvant therapies to distant lymph nodes, facilitating better immunotherapy responses.

cancer biology↗

bioRxiv2025

CNS-Tau Specific Antibodies Illuminate Disease Signatures Across Tauopathies

BackgroundAlternative splicing of the MAPT gene produces distinct tau isoforms in the central and peripheral nervous systems (CNS and PNS), yet their respective biological and pathological roles remain poorly understood. Recent studies suggest that CNS-tau may play a key role in amyloid-{beta} associated neurodegeneration in Alzheimers disease (AD), but the absence of isoform-specific tools has limited both mechanistic insight and biomarker development. We aimed to develop and validate CNS-tau-specific monoclonal antibodies and assess their utility in neuropathology and fluid-based biomarker assays across AD and primary tauopathies. MethodsWe generated six recombinant rabbit monoclonal antibodies targeting a CNS-tau-specific sequence encoded by exons 4 and 5. Specificity and affinity were evaluated via biolayer interferometry, immunoblotting, and tau-expressing HEK293 models. The lead clone, LL-T-1-1, was tested in postmortem brain sections from AD (n = 23), progressive supranuclear palsy (PSP, n = 3), and corticobasal degeneration (CBD, n = 3). A second clone, LL-T-1-5, was optimized for use in plasma assays via an ultrasensitive nanoneedle platform, LoD < 1 pg/ml. ResultsLL-T-1-1 showed nanomolar affinity for CNS-tau and no cross-reactivity with PNS-tau. It selectively labeled dystrophic neurites in AD and all hallmark tau lesions in PSP and CBD without antigen retrieval. LL-T-1-5-based plasma assays revealed CNS-tau levels significantly correlated with cognitive scores (MMSE and QDRS) and differentiated impaired from unimpaired individuals. ConclusionsCNS-tau-specific antibodies LL-T-1-1 and LL-T-1-5 provide new tools for neuropathology and fluid biomarker development across tauopathies.

neuroscience↗

bioRxiv2025

Total variation of quantitative phase map reveals cellular Young's modulus

Collective cell migration is a fundamental physiological process involved in wound healing, development, and tissue regeneration. Though the role of the environmental stiffness in collective cell migration has been extensively investigated, the effects of cellular stiffness have been less studied due to the lack of high-throughput in situ methods for characterizing cellular stiffness. Here, we characterize the cellular Youngs modulus in situ with a large field of view and in real time using use quantitative phase microscopy. We found that standard deviation and total variation of the phase are inversely related to the cellular Youngs modulus, while the total variation of phase has finer mechanical resolution. Integrating the total variation of phase with cell segmentation algorithms, we efficiently analyzed the cellular Youngs modulus for cells in a monolayer. Using this system, we found the cells at the wound frontier are much softer than that of the cells in the inner region of monolayer in in vitro wound healing assay. At single cellular level, the Youngs modulus of leader cells, boundary cells, and inner cells are significantly distinct from each other. To conclude, our method would help elucidate the essential role of cellular stiffness in collective cell migration and has the potential to further benefit the progress of mechanobiology.

biophysics↗

bioRxiv2025

Complete telomere-to-telomere genomes of cowpea reveal insights into centromere evolution in Phaseoleae

Cowpea (Vigna unguiculata) is a versatile legume crop providing a critical source of grain, vegetable and forage globally. Cultivated cowpea is classified into two main subspecies, subsp. sesquipedalis for fresh-pod vegetable and subsp. unguiculata for grain production. Here, we present two complete telomere-to-telomere (T2T) assemblies for the grain-type inbred lines HJD and vegetable-type FC6 through integrating PacBio HiFi reads, Oxford Nanopore ultra-long reads, and Hi-C data. The T2T genomes demonstrated improved contiguity, completeness, and accuracy compared to existing genomes, revealing clear telomeric and centromeric features. Comparative analysis of the T2T genomes highlighted inversions underlying subspecies divergence in cowpea. Evolutionary analysis uncovered contraction of gene families related to symbiosis in HJD, consist with its reduced root nodules compared to FC6. Distribution and composition of tandem repeat arrays and transposable elements in centromeric regions were largely conserved in cowpea, but displayed pronounced variation among Phaseoleae. Furthermore, frequent shifts of centromeric locations coincided with inversions found in Phaseoleae. Overall, this study provides a set of fundamental resources for cowpea improvement and enhances our understanding of cowpea subspecies divergence and genome evolution in Phaseoleae.

genomics↗

bioRxiv2025

PATTY corrects open chromatin bias for improved bulk and single-cell CUT&Tag profiling

Precise profiling of epigenomes is essential for better understanding chromatin biology and gene regulation. Cleavage Under Targets & Tagmentation (CUT&Tag) is an efficient epigenomic profiling technique that can be performed on a low number of cells and at the single-cell level. With its growing adoption, CUT&Tag datasets spanning diverse biological systems are rapidly accumulating in the field. CUT&Tag assays use the hyperactive transposase Tn5 for DNA tagmentation. Tn5s preference toward accessible chromatin alters CUT&Tag sequence read distributions in the genome and introduces open-chromatin bias that can confound downstream analysis, an issue more substantial in sparse single-cell data. We show that open-chromatin bias extensively exists in published CUT&Tag datasets, including those generated with recently optimized high-salt protocols. To address this challenge, we present PATTY (Propensity Analyzer for Tn5 Transposase Yielded bias), a comprehensive computational method that corrects open-chromatin bias in CUT&Tag data by leveraging accompanying ATAC-seq. By integrating transcriptomic and epigenomic data using machine learning and integrative modeling, we demonstrate that PATTY enables accurate and robust detection of occupancy sites for both active and repressive histone modifications, including H3K27ac, H3K27me3, and H3K9me3, with experimental validation. We further develop a single-cell CUT&Tag analysis framework built on PATTY and show improved cell clustering when using bias-corrected single-cell CUT&Tag data compared to using uncorrected data. Beyond CUT&Tag, PATTY sets a foundation for further development of bias correction methods for improving data analysis for all Tn5-based high-throughput assays.

bioinformatics↗

bioRxiv2025

High-resolution spatial analysis reveals pregnenolone metabolism as a potential target for immuno-suppressive microenvironment of BRAF mutant colorectal cancer

BRAF mutant colorectal cancer (CRC) is highly aggressive and often resistant to traditional therapies, presenting a significant challenge in cancer immunotherapy. Understanding the tumor microenvironment (TME) and identifying novel immune checkpoints are crucial for improving treatment outcomes. Here, we employed high-resolution spatial analysis and single-cell RNA sequencing to map the TME of BRAF mutant CRC at single-cell resolution, focusing on the interactions between exhausted CD8+ T cells and C1QC+ macrophages. Mechanistically, we discovered that C1QC+ macrophages drive CD8+ T cell exhaustion through pregnenolone synthesis via the steroidogenic enzyme CYP11A1. Our findings identify pregnenolone metabolism as a previously unrecognized immunosuppressive pathway in BRAF mutant CRC, and suggest that steroid biosynthesis is a generalizable mechanism of immune evasion beyond endocrine-related malignancies. Targeting this pathway offers a promising therapeutic strategy for enhancing anti-tumor immunity in BRAF mutant CRC and potentially other cancers.

cancer biology↗

bioRxiv2025

Legumain drives processing of cathepsins and nuclear localisation of cathepsin L

Lysosomal proteases such as the cathepsin family and the asparaginyl endopeptidase, legumain, govern vital processes to maintain cellular proteostasis, and their dysregulation contributes to diverse pathologies. Recent studies have reported extra-lysosomal localisation of these proteases, especially in the nucleus, cytoplasm, and extracellularly, yet their function is not completely understood. To examine the relationship between legumain and cathepsins, we assessed the activity and expression of cathepsins in wild-type and legumain-deficient (LGMN-/-) cells using chemical activity-based probes and immunoblots. Processing of cathepsins (CTS) L, V, B, and D from the single-chain to the two-chain form was abrogated in the absence of legumain, with some cell type- and species-specific variation observed. This processing was dependent on legumain activity, although the mechanism remains unclear since recombinant legumain does not appear to directly cleave cathepsins in vitro. In cell types where CTSL exists in the nucleus preferentially in its double chain form, loss of legumain led to a reduction in nuclear CTSL levels. To understand the potential role of these lysosomal proteases in the nucleus, we applied our newly refined chemical N-terminomics pipeline, No-enrichment Identification of Cleavage Events (NICE). This analysis revealed widespread changes in both protein abundance and proteolysis, including putative nuclear substrates of CTSL and legumain, that primarily suggest roles in cell proliferation, cell cycle regulation, inflammation, and ribosomal biogenesis. Overall, this study builds on our understanding of the relationship between legumain and cathepsins and provides the first systematic characterisation of lysosomal protease substrates in the nucleus. Our results offer valuable insight into the potential extra-lysosomal roles of these critical proteases.

biochemistry↗

bioRxiv2025

The competition between splicing and 3' processing shapes the human transcriptome

Eukaryotic pre-mRNA processing steps, including splicing and 3' processing, are tightly coordinated, yet the underlying mechanisms remain incompletely understood. U1 snRNP has been proposed to inhibit 3' processing at intronic polyadenylation (IPA) sites through a splicing-independent mechanism termed telescripting. In contrast, we discovered that disrupting splicing--by targeting various key components such as U1 snRNP, U2 snRNP, U2AF, and SF3b--activates 3' processing at thousands of IPA sites. Notably, splicing inhibition, especially of U1 snRNP, induced widespread premature transcription termination within gene bodies through both IPA-coupled and -independent mechanisms. Different splicing factors activated overlapping and distinct sets of IPA sites, reflecting their specific contributions to transcription and spliceosome function. Conversely, inhibition of 3' processing enhanced splicing globally. These findings support a model in which splicing and 3' processing are competing processes that intersect with transcription to shape the transcriptome landscape.

molecular biology↗