Biology subjects

Pan, S.

Publications and source records attributed to Pan, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Entamoeba histolytica Gal/GalNAc lectin intermediate subunit promotes inflammation and epithelial damage in intestinal amebiasis through its C3 region.

Entamoeba histolytica is a common enteric protozoan that sometimes transitions from a symbiont to a pathogen, causing intestinal amebiasis and extraintestinal abscesses in the host. The early-to-intermediate stages of intestinal amebiasis are characterized by an intense inflammatory response, during which host innate immune defenses play an important role. Here, using the cecal infection model of C3H/HeNCrl mice, we performed single-cell RNA sequencing of cecal tissues and identified the prominent pro-inflammatory function of host macrophages in intestinal amebiasis. On the amoebic cell surface, Igl is an intermediate subunit of galactose- and N-acetyl-D-galactosamine-inhibitable lectins, which contributes to parasite adherence. We proposed that E. histolytica Igl diffuses along with amoebic extracellular vesicles and contacts host macrophages, binding to the TLR4 co-receptor MD2 through its C3 region and initiating the TLR4/MyD88/NF-{kappa}B inflammatory signaling pathway in host cells. Moreover, by inducing macrophage inflammation and cytokine production, E. histolytica indirectly impairs intestinal epithelium integrity through the Igl protein. To our knowledge, this is the first report showing a host single-cell atlas in the field of amebiasis research. In response to the parasite invasion during intestinal amebiasis, our study provides new insights elucidating the inflammatory formation and epithelial damage of gut mucosal immune system, and also conduces to the identification of potential drug targets for these amoebas.

microbiology↗

bioRxiv2025

Interferon signaling underlies radiotherapy responses in malignant peripheral nerve sheath tumors (MPNSTs)

Malignant peripheral nerve sheath tumors (MPNSTs) have poor outcomes despite multimodal treatment with surgery, radiation, and systemic therapy. Here, we combine bulk and single cell transcriptomics, genome wide CRISPRi screens, and multiplatform molecular analysis across MPNST cells, mouse allograft models, and human patient samples to understand the mediators of radiation response. Our data reveal MPNSTs induce a type I interferon signature that functionally underlies radiation response. Moreover, irradiation of immunocompetent mouse MPNST allografts leads to interferon mediated T-cell recruitment and activation. Analysis of human MPNST resection specimens demonstrates increased microenvironmental and CD8+ T-cell infiltration are associated with improved local control following radiotherapy while chromosome 9p loss, which harbors an interferon gene cluster, is associated with poor radiotherapy response and decreased CD8+ T-cell infiltration. Taken together, these results provide preclinical rationale for combining immunomodulatory agents targeting interferon signaling to improve radiation responses in MPNSTs, which may be broadly applicable to other soft tissue sarcomas.

cancer biology↗

bioRxiv2025

RNA-triggered fluorescence controlled by RNA switches for real-time RNA expression tracking in living plants

Real-time visualization of RNA dynamics across spatial scales in living plants is desirable yet remains challenging, hindered by the absence of imaging tools that simultaneously offer high sensitivity and deployability in whole living plants. Here, we engineered a modular, RNA-triggered fluorescence (RTF) reporter system de novo for spatiotemporal imaging of RNA from cellular to whole-plant scales in vivo. This system integrates three functional modules: a target-specific allosteric RNA switch, a degradable adapter for background suppression, and a fluorescent reporter. All components are stably expressed from a single vector and assemble in vivo, enabling uniform deployment throughout entire plants. The modified RTF (RTFst) achieves single-molecule sensitivity (signal-to-noise ratio >60) for dynamic tracking of developmentally regulated, tissue-specific, circadian, and stress-responsive mRNAs. Crucially, it enables the first direct, real-time observation of graft-transmissible mRNA trafficking across tissue scales and cross-kingdom transfer of the aphid-secreted long non-coding RNA Ya1 to plant cells. RTF establishes a versatile platform for studying gene regulation, signaling, and transcript mobility in plants, with broad applicability in synthetic biology and crop improvement.

molecular biology↗

bioRxiv2025

Gut microbiota phospholipids regulate intestinal gene expression and can counteract the effects of antibiotic treatment

The gut microbiome influences immune and metabolic homeostasis. Our research using non-obese diabetic (NOD) mice revealed that early-life antibiotic exposure remodels the gut microbiome affecting metabolism and accelerating type 1 diabetes (T1D) incidence, with cecal material transplant (CMT) mitigating the damage. Now examining murine intestinal lipidomic profiles, we identified 747 compounds. Comparing the lipidomic profiles of cecal contents of conventional and germ-free mice and their diets, we identified 87 microbially-produced lipids reduced by antibiotic exposure but CMT-restored. Parallel analysis of human fecal lipid profiles after azithromycin-exposure showed significant alterations with substantial overlap with mice. In vitro co-culture with mouse macrophages or small intestinal epithelial cells and human colonic epithelial cells identified phospholipids that repress inflammation through the NF{kappa}B pathway. Oral administration of these phospholipids to antibiotic-treated NOD mice reduced expression of ileal genes involved in early stages of T1D pathogenesis. These findings indicate potential therapeutic anti-inflammatory roles of microbially-produced lipids.

microbiology↗

bioRxiv2025

Balancing tumour proliferation and sustained cell cycle arrest through proteostasis remodelling drives immune niche compartmentalisation in breast cancer

Uncontrolled proliferation is a hallmark of cancer, yet tumour cells can enter G0 arrest by halting the cell cycle reversibly (quiescence) or irreversibly (senescence) to survive under stress and in hostile tumour microenvironments (TME). G0 arrested cells contribute to drug tolerance, metastasis and recurrence, but their identification remains challenging due to their rarity and elusive regulatory pathways. Here, we quantify G0 arrest and proliferation decisions in single-cell and spatially profiled breast primary tumours to unveil adaptive responses driving immune compartmentalisation. We identify a genomically-constrained and prolonged G0 arrest state resembling that of dormant precursors of cancer progression. This state featured adaptive transcriptional reprogramming, including unfolded protein response stress, reduced mitochondrial translation and epithelial-mesenchymal plasticity enabled by semaphorin signalling. Spatial transcriptomics revealed G0 arrest pockets encapsulated by APOE+ lipid-associated macrophages, myofibroblastic CAFs and immature perivascular cells, suggestive of an immunosuppressive niche contrasting with cytotoxic environments in proliferative hotspots and displaying distinct drug sensitivities. To facilitate future research, we provide a foundation model capturing G0 arrest and proliferation with 94% accuracy in single cell data, available at https://github.com/secrierlab/G0-LM. Our findings provide new insights into the spatial organisation of cell cycle arrest in breast cancer, highlighting the role of G0 states in tumour heterogeneity and adaptation.

cancer biology↗

bioRxiv2024

Cilia dysfunction in the lateral ventricles after neonatal intraventricular hemorrhage does not lead to functional changes in cilia-based CSF flow networks

Intraventricular hemorrhage (IVH) has long been thought to lead to motile cilia dysfunction whereby intraventricular blood breakdown products damage and slough cilia from the ependymal wall. However, specifically how IVH may affect cilia development, structure, and transcriptional activation is not well-understood. Moreover, the impact of blood breakdown product-mediated cilia damage on the functional organization of cilia-based CSF flow networks is unknown. Here, we show hemoglobin exposure affects the number of ciliated ependymal cells in the lateral ventricle (LV) but does not impact in vitro beat frequency of the remaining cilia. Ultrastructurally, IVH decreases the total number of ciliary tufts without impacting axoneme structure. IVH does not result in changes in the expression of cilia-related genes and instead leads to downregulation of neurogenesis markers in parallel with innate immune upregulation. Functionally, we identify three previously uncharacterized cilia-mediated CSF flow domains in the LV lateral wall and show that IVH does not result in widespread disruption of their functional organization. These data de-emphasize cilia as a major contributor to global CSF dysfunction after IVH, and instead call attention to preserving the neurodevelopmental environment and preventing runaway innate immune system activation, as considerations to developing treatment strategies to prevent posthemorrhagic hydrocephalus and other neurodevelopmental sequelae.

neuroscience↗

bioRxiv2024

SLB-msSIM: a spectral library-based multiplex segmented SIM platform for single-cell proteomic analysis

Mass spectrometry (MS)-based single-cell proteomics, while highly challenging, offers unique potential for a wide range of applications to interrogate cellular heterogeneity, trajectories, and phenotypes at a functional level. We report here the development of the spectral library-based multiplex segmented selected ion monitoring (SLB-msSIM) method, a conceptually unique approach with significantly enhanced sensitivity and robustness for single-cell analysis. The single-cell MS data is acquired by multiplex segmented selected ion monitoring (msSIM) technique, which sequentially applies multiple isolation cycles with the quadrupole using a wide isolation window in each cycle to accumulate and store precursor ions in the C-trap for a single scan in the Orbitrap. Proteomic identification is achieved through spectral matching using a well-defined spectral library. We applied the SLB-msSIM method to interrogate cellular heterogeneity in various pancreatic cancer cell lines, revealing common and distinct functional traits among PANC-1, MIA-PaCa2, AsPc-1, HPAF, and normal HPDE cells. Furthermore, for the first time, our novel data revealed the diverse cell trajectories of individual PANC-1 cells during the induction and reversal of epithelial-mesenchymal transition (EMT). Collectively, our results demonstrate that SLB-msSIM is a highly sensitive and robust platform, applicable to a wide range of instruments for single-cell proteomic studies.

systems biology↗

bioRxiv2024

Anti-tumor activity of camptothecin analog conjugate of a RSPO4-based peptibody targeting LGR4/5/6 in preclinical models of colorectal cancer.

Antibody-drug conjugates (ADCs) have emerged as a major modality of targeted cancer therapy, yet no ADC has been approved specifically for colorectal cancer (CRC). LGR4/5/6 (leucine-rich repeat containing, G protein-coupled receptor 4, 5, 6) are three related receptors that are expressed at high levels together or alternately in nearly all cases of CRC. ADCs targeting LGR5 have been shown to have robust anti-tumor potency, but not all CRC cells express LGR5 and LGR5-positive tumor cells may lose LGR5 expression due to cancer cell plasticity. R-spondin 4 (RSPO4) is a natural protein ligand of LGR4/5/6 with high affinity for all three receptors. We fused a mutant form of RSPO4 furin domain that retains high affinity binding to LGR4/5/6 to human IgG1 Fc to create a peptibody designated R462. Conjugation of R462 with a camptothecin analog designated CPT2 at eight drugs per peptibody led to the generation of R462-CPT2 that showed highly potent cytotoxic activity in vitro in CRC cell lines expressing any of LG4/5/6. In cell line xenograft and PDX models of CRC, R462-CPT2 demonstrated robust anti-tumor effect. Importantly, R462-CPT2 showed no major adverse effect at therapeutically effective dose levels. These results strongly support the use of RSPO ligand drug-conjugates that target LGR4/5/6 simultaneously for the treatment of CRC.

pharmacology and toxicology↗

bioRxiv2024

Classifying epithelial-mesenchymal transition states in single cell cancer data using large language models

Single-cell foundation models (scFMs) have been widely adopted for cell type annotation, yet their suitability for modelling cellular plasticity, where cells transition along continuous, context-dependent state trajectories, remains unclear. Here, we systematically benchmark state-of-the-art scFMs against conventional machine learning and bioinformatics approaches on epithelial-mesenchymal plasticity (EMP), a prototypical plastic cellular process. We show that naive fine-tuning of scFMs often fails to resolve intermediate states and is strongly influenced by tissue- and stimulus-specific signals. We propose a parameter-efficient dual-task adaptation strategy for EMP foundation models (EMP-FM) that combines discrete classification with pseudotime-guided regression, which improves cell state resolution in controlled settings (up to 85% AUROC), but remains sensitive to domain shifts. Across diverse in vitro and in vivo datasets, scFMs do not consistently outperform conventional methods, which often achieve comparable performance with lower complexity. Together, our results delineate both the potential and current limitations of scFMs for modelling cellular plasticity and support their complementary use alongside established bioinformatics approaches.

bioinformatics↗

bioRxiv2024

PURE-seq identifies Egr1 as a Potential Master Regulator in Murine Aging by Sequencing Long-Term Hematopoietic Stem Cells

Single-cell transcriptomics is valuable for uncovering individual cell properties, particularly in highly heterogeneous systems. However, this technique often results in the analysis of many well- characterized cells, increasing costs and diluting rare cell populations. To address this, we developed PURE-seq (PIP-seq for Rare-cell Enrichment and Sequencing) for scalable sequencing of rare cells. PURE-seq allows direct cell loading from FACS into PIP-seq reactions, minimizing handling and reducing cell loss. PURE-seq reliably captures rare cells, with 60 minutes of sorting capturing tens of cells at a rarity of 1 in 1,000,000. Using PURE-seq, we investigated murine long- term hematopoietic stem cells and their transcriptomes in the context of hematopoietic aging, identifying Egr1 as a potential master regulator of hematopoiesis in the aging context. PURE-seq offers an accessible and reliable method for isolating and sequencing cells that are currently too rare to capture successfully with existing methods.

bioengineering↗

bioRxiv2024

Multiplatform molecular profiling and functional genomic screens identify prognostic signatures and mechanisms underlying MEK inhibitor response in somatic NF1 mutant glioblastoma

NF1 is recurrently mutated in glioblastoma yet the molecular landscape and efficacy of targeted therapies remain unclear. Here, we combine bulk and single cell genomics of human somatic NF1 mutant, IDH-wildtype glioblastomas with functional genomic analysis of cell lines and mouse intracranial tumor models to identify molecular subgroups within NF1 mutant glioblastomas and mechanisms underlying MEK inhibitor response. Targeted DNA sequencing showed homozygous deletion of the cell cycle regulator CDKN2A/B is a poor prognostic marker in somatic NF1 mutant, but not NF1 wildtype, tumors. DNA methylation array profiling revealed three epigenetic groups highlighted by distinct clinical features, co-mutation patterns, and reference methylation classifier identities. Genome-wide CRISPRi screens in glioblastoma cells revealed cell cycle regulators are conserved mediators of cell growth while response to the MEK inhibitor selumetinib converges on Ras/RAF/MEK pathway activation. Repression of the RAF regulator SHOC2 sensitizes glioblastomas to selumetinib in vitro and in vivo in mouse intracranial glioblastoma models. Single cell RNA-sequencing of mouse intracranial glioblastomas treated with the MEK inhibitor selumetinib reveals distinct responses between mesenchymal-like (MES-like) and non MES-like subpopulations suggesting non-MES like cells are intrinsically resistant to MEK inhibition. Finally, single nuclear RNA-sequencing (snRNA-seq) of human NF1 mutant, CDKN2A/B deleted glioblastomas reveals MES-like tumor cells are associated with selumetinib sensitivity signatures while non MES-like cells exhibit increased cell cycle progression and lack selumetinib sensitivity, further supporting the notion that MEK inhibition specifically targets MES-like tumor cell subpopulations. Taken together, our data underscores the heterogeneity between and within somatic NF1 mutant glioblastomas and delineates mechanisms of MEK inhibitor response across distinct tumor subpopulations, guiding the development of future therapeutic strategies that may synergize with MEK inhibition for NF1 mutant tumors. The tumor suppressor NF1 is mutated in 15% of glioblastomas,1-3 the most common malignant brain tumor with poor outcomes and few effective treatments.4 NF1 is a GTPase activating protein (GAP) that negatively regulates Ras, and thus, NF1 loss leads to induction of Ras/RAF/MEK/ERK signaling, driving tumorigenesis and comprising a targetable molecular cascade.5,6 Genomic analysis of glioblastoma demonstrates NF1 mutation is associated with a mesenchymal-like (MES-like) transcriptomic tumor cell subpopulation and altered tumor microenvironment.7,8 More broadly, DNA methylation analysis reveals multiple epigenetic subgroups with overlapping relationships to transcriptomic subtype and DNA alterations, underscoring the complex relationship between genetic drivers and molecular signatures.9 While the updated 2021 Central Nervous System WHO tumor classification incorporates an ever increasing amount of molecular criteria for diffuse astrocytic tumors,10 the existence and clinical significance of molecular subgroups within somatic NF1 mutant, IDH-wildtype glioblastomas based on genetic co-mutations, epigenetic profile, or transcriptomic signatures remain unclear. Preclinical data support the utility of MEK inhibition in NF1 mutant gliomas,11,12 and the MEK inhibitor selumetinib is FDA approved for tumors arising in patients with syndromic neurofibromatosis type 1 (NF-1) harboring a germline NF1 mutation.13,14 In NF-1 associated gliomas, MEK inhibition demonstrates efficacy in a limited case series,15 and combined BRAF/MEK inhibition shows efficacy in BRAF p.V600E mutant gliomas,16 further supporting the translational potential of Ras/Raf/MEK/ERK blockade within genetically defined glioma subtypes. Nevertheless, treatment resistance to molecular monotherapy remains a challenge,17-20 and the mechanisms underlying MEK inhibitor resistance in NF1 mutant glioma are unknown. Here, we integrate targeted DNA sequencing, DNA methylation profiling, and single nuclear RNA-sequencing (snRNA-seq) of human patient somatic NF1 mutant, IDH-wildtype glioblastomas with single cell RNA-sequencing (scRNA-seq), genome-wide clustered regularly interspaced short palindromic repeats interference (CRISPRi) screens, and pharmacologic studies in cell lines and mouse intracranial glioblastoma models to define molecular subgroups and functional mediators of MEK inhibitor response. Targeted DNA sequencing of NF1 mutant, IDH-wildtype glioblastomas (n=186 tumors) revealed CDKN2A/B deletion was associated with poor outcomes in NF1 mutant, but not NF1 wildtype, glioblastomas. DNA methylation profiling (n=129 tumors) demonstrated three epigenetic subgroups with distinct clinical features, co- mutation patterns across cell cycle genes, and reference methylation classifier identities. Genome-wide CRISPRi screens in mouse SB28 and human GBM43 glioblastoma cells identified a conserved cell cycle gene network mediating cell growth, consistent with the clinical importance of additional hits affecting the cell cycle in human somatic NF1 mutant glioblastomas. Moreover, genome-wide mediators of selumetinib response converged upon two Ras pathway effectors mediating selumetinib sensitivity: BRAF and SHOC2. SHOC2 repression in glioblastoma cells significantly improved selumetinib response both in vitro and in intracranial allografts in vivo. Single cell RNA-sequencing (scRNA-seq) of mouse intracranial glioblastomas treated with the MEK inhibitor selumetinib revealed MES-like tumor cells correlated with CDKN2A retention and the CRISPRi screen selumetinib sensitivity signature, with selumetinib resistant cells displaying Ras pathway induction. In contrast, non-MES like tumor cells were CDKN2A deficient and lacked expression of the CRISPRi screen selumetinib sensitivity signature, with selumetinib resistant cells inducing a glial de-differentiation program. Finally, snRNA-seq of NF1 mutant, CDKN2A/B deleted, IDH-wildtype glioblastomas (n=9) showed non MES-like tumor cells exhibit increased cell cycle progression and were not associated with the CRISPRi screen selumetinib sensitivity signature. MES-like tumor cells within newly diagnosed, but not recurrent, tumors retained expression of the CRISPRi screen selumetinib sensitivity signature, suggesting resistance can arise both between and within specific transcriptomic glioblastoma cell tumor cell subpopulations. Taken together, our data identifies clinically important subgroups of NF1 mutant, IDH-wildtype glioblastomas and supports a model in which heterogeneity between tumors and within tumor cell subpopulations underlies MEK inhibitor response, supporting the need for additional synergistic therapeutic approaches beyond maximal Ras pathway blockade for NF1 mutant glioblastomas.

genomics↗

bioRxiv2024

Intestinal microbiome dysbiosis increases Mycobacteria pulmonary colonization in mice by regulating the Nos2-associated pathways

AbstractIncreasing researches reveal gut microbiota was associated with the development of tuberculosis. How to prevent or reduce Mycobacterium tuberculosis colonization in the lungs is a key measure to prevent tuberculosis. However, the data on gut microbiota preventing Mycobacterium colonization in the lungs were scarce. Here, we established the clindamycin-inducing intestinal microbiome dysbiosis and fecal microbial transplantation models in mice to identify gut microbiotas effect on Mycobacteriums colonization in the mouse lungs and explore its potential mechanisms. The results showed that clindamycin treatment altered the diversity and composition of the intestinal bacterial and fungal microbiome, weakened the trans-kingdom network interactions between bacteria and fungi, and induced gut microbiome dysbiosis in the mice. Gut microbiota dysbiosis increases intestinal permeability and enhances the susceptibility of Mycobacterium colonization in the lungs of mice. The potential mechanisms were gut microbiota dysbiosis altered the lung transcriptome and increased Nos2 expression through the "gut-lung axis". Nos2 high expression disrupts the intracellular antimicrobial and anti-inflammatory environment by increasing the concentration of NO, decreasing the levels of ROS and Defb1 in the cells, and resulting in promoting Mycobacteria colonization in the lungs of mice. The present study raises a potential strategy for reducing the risks of Mycobacteria infections and transmission by regulating the gut microbiome balance.

microbiology↗

bioRxiv2024

NovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing

De novo peptide sequencing is a fundamental research area in mass spectrometry (MS) based proteomics. However, those methods have often been evaluated using a couple of simple metrics that do not fully reflect their overall performance. Moreover, there has not been an established method to estimate the false discovery rate (FDR) and the significance of de novo peptide-spectrum matches (PSMs). Here we propose NovoBoard, a comprehensive framework to evaluate the performance of de novo peptide sequencing methods. The framework consists of diverse benchmark datasets (including tryptic, nontryptic, immunopeptidomics, and different species), and a standard set of accuracy metrics to evaluate the fragment ions, amino acids, and peptides of the de novo results. More importantly, a new approach is designed to evaluate de novo peptide sequencing methods on target-decoy spectra and to estimate their FDRs. Our results thoroughly reveal the strengths and weaknesses of different de novo peptide sequencing methods, and how their performances depend on specific applications and the types of data. Our FDR estimation also shows that some tools may perform better than the others in distinguishing between de novo PSMs and random matches, and can be used to assess the significance of de novo PSMs.

bioinformatics↗

bioRxiv2024

Protein SUMOylation promotes cAMP-independent EPAC1 activation

Exchange protein directly activated by cAMP (EPAC1) mediates the intracellular functions of a critical stress-response second messenger, cAMP. Herein, we report that EPAC1 is a cellular substrate of protein SUMOylation, a prevalent stress-response posttranslational modification. Site-specific mapping of SUMOylation by mass spectrometer leads to identifying K561 as a primary SUMOylation site in EPAC1. Sequence and site-directed mutagenesis analyses reveal a functional SUMO-interacting motif required for cellular SUMOylation of EPAC1. SUMO modification of EPAC1 mediates its heat shock-induced Rap1/2 activation in a cAMP-independent manner. Structural modeling and molecular dynamics simulation studies demonstrate that SUMO substituent on K561 of EPAC1 promotes Rap1 interaction by increasing the buried surface area between the SUMOylated receptor and its effector. Our studies identify a functional SUMOylation site in EPAC1 and unveil a novel mechanism in which SUMOylation of EPAC1 leads to its autonomous activation. The findings of SUMOylation-mediated activation of EPAC1 not only provide new insights into our understanding of cellular regulation of EPAC1 but also will open up a new field of experimentation concerning the cross-talk between cAMP/EPAC1 signaling and protein SUMOylation, two major cellular stress response pathways, during cellular homeostasis.

cell biology↗

bioRxiv2023

Allocator is a graph neural network-based framework for mRNA subcellular localization prediction

MotivationThe asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular processes. To advance our comprehension of gene regulatory networks, it is essential to develop computational tools for accurately identifying the subcellular localizations of mRNAs. However, considering multi-localization phenomena remains limited in existing approaches, with none considering the influence of RNAs secondary structure. ResultsIn this study, we propose Allocator, a multi-view parallel deep learning framework that seamlessly integrates the RNA sequence-level and structure-level information, enhancing the prediction of mRNA multi-localization. The Allocator models equip four efficient feature extractors, each designed to handle different inputs. Two are tailored for sequence-based inputs, incorporating multilayer perceptron and multi-head self-attention mechanisms. The other two are specialized in processing structure-based inputs, employing graph neural networks. Benchmarking results underscore Allocators superiority over state-of-the-art methods, showcasing its strength in revealing intricate localization associations. AvailabilityThe webserver of Allocator is available at http://Allocator.unimelb-biotools.cloud.edu.au; the source code and datasets are available at https://github.com/lifuyi774/Allocator

bioinformatics↗

bioRxiv2023

Human brain glycoform co-regulation network and glycan modification alterations in Alzheimer's disease

Despite the importance of protein glycosylation to brain health, current knowledge of glycosylated proteoforms or glycoforms in human brain and their alterations in Alzheimers disease (AD) is limited. Here, we present a new paradigm of proteome-wide glycoform profiling study of human AD and control brains using intact glycopeptide-based quantitative glycoproteomics coupled with systems biology. Our study identified over 10,000 human brain N-glycoforms from nearly 1200 glycoproteins and uncovered disease signatures of altered glycoforms and glycan modifications, including reduced sialylation and N-glycan branching as well as elevated mannosylation and N-glycan truncation in AD. Network analyses revealed a higher-order organization of brain glycoproteome into networks of co-regulated glycoforms and glycans and discovered glycoform and glycan modules associated with AD clinical phenotype, amyloid-{beta} accumulation, and tau pathology. Our findings provide novel insights and a rich resource of glycoform and glycan changes in AD and pave the way forward for developing glycosylation-based therapies and biomarkers for AD.

neuroscience↗

bioRxiv2023

Systems genetics identifies the association between Enc1 and cognitive function in the hippocampus

Ectodermal-Neural Cortex 1 (ENC1) is expressed in multiple regions of the brain, including the hippocampus. However, knowledge about its function has been well explored only in the context of peroxidative stress and cancer. In this study, we investigated the association of hippocampal Enc1 with cognitive function in BXD mice. We performed Pearson correlation, phenotype-wide association analysis (PheWAS), expression-Based PheWAS, pathway enrichment, and protein interaction networks on Enc1 and BXD phenotypes/transcriptome of the hippocampus, and the results indicated that Enc1 is inextricably linked to cognitive performance. In addition, we found that most of the Enc1 co-expressed genes were highly expressed in GABAergic neuronal cells. Expression quantitative trait loci analysis indicated that Enc1 was cis-regulated in the hippocampus of mice as well as human. Genome-wide association analysis revealed ENC1 to be significantly associated with cognitive-related traits, including age-related cognitive changes etc. In conclusion, our findings demonstrated that Enc1 is involved in cognitive functions mainly in hippocampal GABAergic neuronal cells through neurogenesis, synaptic signaling, and CGMP-PKG signaling pathways, and interacts with the neurological function-related genes.

genetics↗

bioRxiv2023

PSICHIC: physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data

In drug discovery, determining the binding affinity and functional effects of small-molecule ligands on proteins is critical. Current computational methods can predict these protein-ligand interaction properties but often lose accuracy without high-resolution protein structures and falter in predicting functional effects. We introduce PSICHIC (PhySIcoCHemICal graph neural network), a framework uniquely incorporating physicochemical constraints to decode interaction fingerprints directly from sequence data alone. This enables PSICHIC to attain first-of-its-kind emergent capabilities in deciphering mechanisms underlying protein-ligand interactions, achieving state-of-the-art accuracy and interpretability. Trained on identical protein-ligand pairs without structural data, PSICHIC matched and even surpassed leading structure-based methods in binding affinity prediction. In a library screening for adenosine A1 receptor agonists, PSICHIC discerned functional effects effectively, ranking the sole novel agonist within the top three. PSICHICs interpretable fingerprints identified protein residues and ligand atoms involved in interactions. We foresee PSICHIC reshaping virtual screening and deepening our understanding of protein-ligand interactions.

bioinformatics↗