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Zhang, B.

Publications and source records attributed to Zhang, B..

At least 181 records · Page 10Linked to original sources

Cortactin regulates metastatic dormancy of circulating tumor cells by suppressing mTOR-dependent senescence

Metastatic dormancy often refers to the stable cell cycle arrest of disseminated tumor cells (DTCs) at distant sites. However, whether circulating tumor cells (CTCs) in the blood microenvironment can enter a dormant state prior to extravasation and becoming DTCs remains unclear. Using patient-derived melanoma CTC lines and animal explant models (CDX), we identified a previously unrecognized role of the cytoskeletal regulator cortactin (encoded by CTTN) in controlling mTOR/p53-dependent senescence and metastatic dormancy. Cortactin was localized to Rab7-postive endosomes and engaged in late endosomal tethering and homeostasis. The depletion of cortactin resulted in the accumulation of aberrantly enlarged late endosomal aggregates that were positive for Rab7 and mTOR. The mTOR protein complex was accumulated and activated within these abnormal vesicular structures, leading to robust p53 activation through phosphorylation at serine (S) 15 and S33 sites. Consequently, melanoma CTCs underwent G0/G1 cell cycle arrest and entered cellular senescence. This unusual oncogene-induced senescence (OIS) mechanism was characterized by SASP upregulation, {beta}-galactosidase activity, depletion of Ki-67 and Lamin B1, and elevated mitochondrial ROS (mtROS) levels. Notably, a positive feedback loop between p53 and mtROS was essential for maintaining stable senescence in CTCs. In preclinical CDX mouse models, we developed a sequential therapeutic strategy combining cortactin depletion with anti-Bcl-xL senolytic drugs. Such "One-two punch" treatment strategy effectively eliminated viable CTCs and suppressed metastatic tumor growth in vivo. Thus, targeting cortactin to induce CTC senescence, followed by senolytic therapy, may represent a promising strategy to block CTC-mediated metastatic progression.

cancer biology↗

Phase separation of Polycomb-like (PCL) proteins drive PRC2 complex condensates to regulate gene expression

Polycomb group (PcG) proteins function as two major multicomponent protein complexes: Polycomb repressive complex 1 (PRC1) and 2 (PRC2) to repress key developmental genes and maintain epigenetic memory of cell identity during development. Phase-separation has long been implicated in PRC1 mediated gene silencing, but it is still unclear whether PRC2 also utilize a similar mechanism to regulate gene expression. Here we report that Polycomb-like (PCL) proteins, PRC2 accessory factors, can phase-separate in vitro and generate dynamic puncta in vivo. Biochemical and cellular analyses reveal that PCL proteins (hereafter referred to as PCLs) have intramolecular interaction between N- and C-terminal domains, which make PCLs into more compact conformations. The intramolecular interaction not only controls the size of the PCLs phase separation droplets, but also affects the chromatin association of PRC2. Finally, we show that CpG islands, key DNA regulatory elements in mammalian promoters, disrupt the N-C intramolecular interaction of PCLs to expose their middle intrinsically disordered regions (IDRs), which in turn trigger PCLs driven PRC2 condensates formation. Together, this study provides a new perspective on the regulation of PRC2 by PCLs, implicating PCLs read CpG islands to fine-tune their oligomerization to overcome the threshold for PRC2 recruitment to corresponding genomic loci via multivalent interaction with CpG islands chromatin.

biochemistry↗

CompBioAgent: an LLM-powered agent for single-cell RNA-seq data exploration

AO_SCPLOWBSTRACTC_SCPLOWAdvancements in high-throughput biological technologies, particularly single-cell RNA sequencing (scRNA-seq), have generated vast amounts of complex data that offer valuable insights into gene expression, cellular behavior, and disease mechanisms. However, the analysis of such data often requires specialized computational skills and expertise, which can pose a barrier to many researchers. To address this challenge, we developed CompBioAgent, a user-friendly web application designed to democratize access to bioinformatics resources, powered by Large Language Models (LLMs). By integrating with the CellDepot, CompBioAgent allows users to easily query and explore gene expression data related to various diseases, cell types, and experimental conditions. Moreover, the tool employs Cellxgene Visualization In Plugin (Cellxgene VIP) platform to generate a range of intuitive visualizations, including violin plots, UMAP embeddings, heatmaps, etc. With its natural language interface, CompBioAgent automatically converts scientific queries into structured data requests and returns the plot of interest, enabling seamless exploration of biological data without the need for programming expertise. Such integration enhances the ability of researchers to visualize complex biological insights and identify key patterns, making high-level data analysis more accessible and efficient. A demo website and a list of examples are available at https://celldepot.bxgenomics.com/compbioagent, and the source code is released at https://github.com/interactivereport/compbioagent.

bioinformatics↗

Inhibition of DHODH Activates Pyroptosis and cGAS-STING Pathways to Enhance NK cell Infiltration Mediated Anti-tumor Immunity in Melanoma

Cancer cells are heavily reliant on de novo pyrimidine synthesis. Suppression of pyrimidine metabolism directly inhibits tumor growth and fosters immune activation within the tumor microenvironment. Dihydroorotate dehydrogenase (DHODH), a crucial enzyme governing de novo pyrimidine synthesis, is a critical player in this context. Inhibition of DHODH not only reverses immunosuppression but also instigates a mild innate immune response. However, the impact of DHODH inhibition on natural killer (NK) cells remains unexplored. In this study, we found that inhibition of DHODH efficiently promotes NK cells infiltration in tumors. Suppression of DHODH led to increased oxidative stress in mitochondria, the release of mtDNA, and activation of caspase 3, which in turn activated the cGAS-STING pathway and pyroptosis in cancer cells, respectively, contributing to NK cells induced antitumor immune responses in melanoma. Additionally, we developed EA6, a novel DHODH inhibitor with higher efficacy in promoting NK cells infiltration. In summary, this study underscores that modulation of pyrimidine metabolism can effectively trigger antitumor immune responses, with a specific emphasis on NK cells. This finding opens new avenues for enhancing the efficacy of targeted nucleotide metabolism in cancer therapy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/644471v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@88d4fcorg.highwire.dtl.DTLVardef@156fe1aorg.highwire.dtl.DTLVardef@448086org.highwire.dtl.DTLVardef@152079c_HPS_FORMAT_FIGEXP M_FIG C_FIG The anti-tumor mechanisms of DHODH inhibition. Inhibition of DHODH activates cGAS-STING pathways to enhance NK cell infiltration. And the tumor-infiltrating NK cells facilitate melanoma cells pyroptosis which providing a positive feedback mechanism for DHODH-mediated anti-tumor immunity.

cancer biology↗

Homoharringtonine Promotes FTO Degradation to Suppress LILRB4-Mediated Immune Evasion in Acute Monocytic Leukemia

Acute monocytic leukemia (AML-M5), a subtype of acute myeloid leukemia, is a highly aggressive malignancy characterized by a poor prognosis, primarily due to the ability of leukemic cells to evade immune surveillance. In this study, we demonstrate that homoharringtonine (HHT), an FDA-approved therapeutic agent for chronic myeloid leukemia (CML), inhibits this immune evasion by targeting the FTO/m6A/LILRB4 signaling pathway in monocytic AML. Utilizing RNA sequencing (RNA-seq) and various functional assays, we reveal that HHT treatment significantly reduces LILRB4 expression at both the RNA and protein levels, suggesting that the effects of HHT on LILRB4 are distinct from its well-established role as a protein synthesis inhibitor. Mechanistically, HHT treatment markedly increases global levels of RNA m6A in THP-1 cells by promoting the degradation of FTO, which subsequently diminishes the expression of its downstream targets, MLL1 and LILRB4. Furthermore, in vitro and in vivo analyses employing monocytic AML cell lines, mouse-derived AML xenograft models, and patient samples collectively support the conclusion that HHT suppresses immune evasion in monocytic AML by reducing LILRB4 expression. Importantly, the downregulation of LILRB4 resulting from HHT treatment enhances the susceptibility of THP-1 cells to CD8+ T cell cytotoxicity, accompanied by increased markers of immune activation. Overall, our findings position HHT as a promising clinical agent for enhancing CD8+ T cell-based cancer immunotherapy by mitigating immune evasion in monocytic AML. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/643466v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@e72e5dorg.highwire.dtl.DTLVardef@19519aeorg.highwire.dtl.DTLVardef@1c8f786org.highwire.dtl.DTLVardef@f2a963_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Endothelial Cept1 Promotes Post-Ischemic Angiogenesis in a Pparα-Dependent Fashion

BackgroundCept1 is essential for de novo phopholipogenesis and is impacted by diabetes. We previously demonstrated that conditional knockdown of Cept1 in the endothelium leads to reduced hindlimb angiogenesis and tissue recovery. We hypothesized that Cept1 may also be sufficient in promoting post-ischemic angiogenesis and recovery in the setting of diabetes. MethodsCEPT1 content was evaluated in peripheral arteries of patients with peripheral arterial disease (PAD), and with or without diabetes. An endothelial cell (EC)-specific Cept1 overexpression mouse model was developed (Cept1fl/flCre+) in adult C57BL6 mice. Murine aortae were harvested, for single-cell RNA sequencing (scRNA-seq), and unilateral hindlimb ischemia was used to evaluate angiogenesis in Cept1fl/flCre+ mice. Primary ECs were isolated and HUVECs transduced with Cept1 cDNA were developed, and evaluated using molecular assays, in vitro functional assays, and mass spectrometry. ResultsIn humans, arterial intima CEPT1 was elevated in the setting of PAD and diabetes, along with ACOX1, VEGF2R, p-Akt, and p-eNOS. In mice, scRNA-seq demonstrated that ECs with Cept1 overexpression were enriched with wound healing, angiogenesis, sprouting, and cell migration pathways. Diabetic Cept1fl/flCre+ mice had improved hind-limb perfusion and angiogenesis, and their aortic rings had increased ex vivo capillary sprouting. Cept1 overexpression in ECs significantly increased migration, tubule formation, and proliferation as predicted by scRNA-seq. Cept1 overexpression in ECs led to increased Ppar, Acox1, Vegfa, and Vegf2r. Similarly, treatment with siPpar, and inhibitors for PPAR (GW6471), VEGFR2 (ZM323881), Akt (LY294002), and eNOS (L-NAME) abrogated CEPT1-induced EC migration. ConclusionsCept1 overexpression promotes EC function and post-ischemic recovery. The impact of CEPT1 on ECs is at least in part dependent on p-Akt/p-eNOS angiogenic signaling and PPAR. Since CEPT1 is elevated in diseased human peripheral arterial tissue, these findings suggest that CEPT1 may be playing an important compensatory role in vascular recovery and reperfusion following ischemic injury in the setting diabetes. HighlightsO_LICEPT1 content is higher in the peripheral arteries of individuals with peripheral arterial disease (PAD) and type 2 diabetes. C_LIO_LICept1 over expression induces endothelial cell activation and function and enhances post-ischemia angiogenesis in vivo. C_LIO_LICEPT1 induces endothelial pAkt/p-eNOS signaling and VEGF-A production in a PPAR dependent fashion. C_LIO_LICEPT1 may be an important regenerative signal that is increased in the peripheral arteries in the setting of PAD. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/642511v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@dde6ecorg.highwire.dtl.DTLVardef@63c6c4org.highwire.dtl.DTLVardef@8e753dorg.highwire.dtl.DTLVardef@b314cd_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

AAV-mediated ARSA replacement for the treatment of Metachromatic Leukodystrophy

Metachromatic leukodystrophy (MLD) is an autosomal recessive neurodegenerative disorder caused by mutations in the arylsulfatase A (ARSA) gene, resulting in lower sulfatase activity and the toxic accumulation of sulfatides in the central and peripheral nervous system. Children account for 70% of cases and become progressively disabled with death occurring within 10 years of disease onset. Gene therapy approaches to restore ARSA expression via adeno-associated viral vectors (AAV) have been promising but hampered by limited brain biodistribution. We report the development of a novel capsid AAV.GMU01, demonstrating superior biodistribution and transgene expression in the central nervous system of non-human primates (NHPs). Next, we show that AAV.GMU01-ARSA treated MLD mice exhibit persistent, normal levels of sulfatase activity and a concomitant reduction in toxic sulfatides. Treated mice also show a reduction in MLD-associated pathology and auditory dysfunction. Lastly, we demonstrate that treatment with AAV.GMU01-ARSA in NHPs is well-tolerated and results in potentially therapeutic ARSA expression in the brain. In summary, we propose AAV.GMU01-ARSA mediated gene replacement as a clinically viable approach to achieve broad and therapeutic levels of ARSA.

neuroscience↗

CHIEF: An Attention-based Ensemble Learning Framework for Functional Protein Design

Protein de novo design is a longstanding challenge in biological field due to the multifaceted physicochemical properties and complexities of proteins. Several deep learning models have emerged for protein de novo design. However, each model exhibits distinct strengths and limitations because of the differences in training strategies or neural network architectures. Therefore, improving the effectiveness of protein design, particularly for functional protein, requires further improvement. To tackle this challenge, we developed CHIEF (Chimera Ensemble Inverse Folding), an attention-based ensemble framework that integrates five pretrained base models (ProteinMPNN-vanilla, ProteinMPNN-soluble, ESM-IF, Frame2seq and PiFold) to leverage their complementary strengths and mitigate limitations. Compared with the base models, CHIEF significantly improved the sequence recovery rate by 16.6-28.0%, while reducing the prediction perplexity by 22.7-34.6%. CHIEF also exhibited superior protein-designing capacity in variable sequence- and structure-based metrics and in large and complex proteins. CHIEF dynamically captured the semantic information from base models in a context-dependent manner and was minimally affected by the ablation of each base model. More importantly, CHIEF demonstrates real-world applicability to design functional malate dehydrogenase (MDH), achieving a 100% success rate. In summary, our study develops an ensemble deep learning model that improves the efficacy of protein sequence design, and will be a valuable platform for protein engineering and drug development.

bioengineering↗

Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE

Recent advances in spatial transcriptomics (ST) technologies have transformed our ability to profile gene expression while retaining the crucial spatial context within tissues. However, existing ST platforms suffer from high costs, long turnaround times, low resolution, limited gene coverage, and small tissue capture areas, which hinder their broad applications. Here we present iSCALE, a method that predicts super-resolution gene expression and automatically annotates cellular-level tissue architecture for large-sized tissues that exceed the capture areas of standard ST platforms. The accuracy of iSCALE were validated by comprehensive evaluations, involving benchmarking experiments, immunohistochemistry staining, and manual annotation by pathologists. When applied to multiple sclerosis human brain samples, iSCALE uncovered lesion associated cellular characteristics that were undetectable by conventional ST experiments. Our results demonstrate iSCALEs utility in analyzing large-sized tissues with automatic and unbiased tissue annotation, inferring cell type composition, and pinpointing regions of interest for features not discernible through human visual assessment.

genomics↗

Drug repurposing reveals Posaconazole as a CYP11A1 inhibitor enhancing anti-tumour immunity

Steroid hormones regulate cell physiology and immune function, with dysregulated steroidogenesis promoting cancer progression by supporting tumour growth and suppressing anti-tumour immunity. Targeting CYP11A1, the first and rate-limiting enzyme in steroid biosynthesis, has shown promise in cancer therapy, but safe and effective inhibitors remain an unmet need. Undertaking in silico structure-based drug repurposing approach, we found Posaconazole as an inhibitor of CYP11A1. The docking pose analysis showed that Posaconazole can form multiple hydrogen bonds and hydrophobic interactions with the key residues at the binding site and the cofactor, stabilising the protein-ligand complex. We validated its inhibition efficiency in cell-based assays. In a mouse model of lung metastasis, we demonstrated that Posaconazole restricts metastatic cancer growth by stimulating anti-tumour immunity. These findings highlight Posaconazoles potential as a research tool to study steroidogenesis and as a candidate for further preclinical and clinical evaluation in pathological conditions associated with local steroid production, such as steroidogenic tumours.

immunology↗

Glycogen Engineering Improves the Starvation Resistance of Mesenchymal stem cells and their Therapeutic Efficacy in Pulmonary Fibrosis

Mesenchymal stem cells (MSCs) are widely used in regenerative medicine, including the treatment of pulmonary fibrosis. However, implanted MSCs disappear within days, constraining therapeutic efficacy, which is largely attributed to nutrient deprivation. In this study, we established glycogen metabolism engineering strategies in mammalian cells. By expressing a functionally optimized glycogen synthase (GYSmut), MSCs could accumulate large amounts of glycogen rapidly as a reserve substance. Glycogen engineering significantly improved the survival of MSCs during starvation both in vitro and in vivo, enhancing cell viability post-implantation and their therapeutic efficacy in pulmonary fibrosis. Glycogen-engineered MSCs may serve as chassis cells for further applications. Our research highlights the importance of glucose metabolism regulation in cell-based therapy and demonstrates the great potential for the metabolic engineering of MSCs and other therapeutic cells.

bioengineering↗

Cell surface proteomics of patient-derived malignant rhabdoid tumor organoids identifies ROBO1 as potential CAR T cell target for pediatric solid tumors.

Malignant rhabdoid tumors are highly aggressive pediatric malignancies with limited treatment options and poor outcomes. To expand therapeutic options, we employed mass spectrometry-based cell surface proteomics on malignant rhabdoid tumor and patient-matched normal kidney organoids to identify potential CAR T cell targets. Integrating these findings with transcriptomics and protein expression data, we revealed ROBO1 as a promising target, showing strong and uniform expression across malignant rhabdoid and other pediatric tumors. ROBO1-targeted CAR T cells displayed potent anti-tumor activity in vitro, effectively eliminating tumor cells in co-cultures with organoids from malignant rhabdoid tumors, rhabdomyosarcoma, and neuroblastoma. In vivo, ROBO1 CAR T cells infiltrated tumors, induced potent tumor regression and significantly increased survival in malignant rhabdoid tumor-bearing mice. These findings establish ROBO1 as a compelling therapeutic target for CAR T cell therapy and offer a promising approach to address the critical need for effective treatments in high-risk pediatric solid tumors. Statement of significanceThis study identifies ROBO1 as a promising CAR T cell target for pediatric solid tumors. Using patient-derived tumor organoids and tissues, we demonstrate strong ROBO1 expression across several tumor entities and robust anti-tumor efficacy of ROBO1-targeted CAR T cells in vitro and in vivo, underscoring its potential for clinical translation.

cancer biology↗

Endogenously generated Dutch-type Aβ nonfibrillar aggregates dysregulate presynaptic neurotransmission in the absence of detectable inflammation

Structured AbstractO_ST_ABSBackgroundC_ST_ABSAPPE693Q ("Dutch") transgenic mice develop aging-related learning deficits and accumulate endogenously generated nonfibrillar aggregates of A{beta} (NFA-A{beta}) and APP -carboxy terminal fragments. NFA-A{beta} correlates with synaptic loss and memory deficits more closely than does fibrillar A{beta}. MethodsWe assessed the physiological, transcriptomic, ultrastructural, histological, and metabolic changes associated with the accumulation of NFA of Dutch A{beta} in brains of APPE693Q mice. ResultsAging-related accumulation of NFA-A{beta} in APPE693Q mice was revealed by A11 immunohistochemistry and cyclic D,L--peptide-FITC microscopy. Presynaptic termini of APPE693Q mice developed physiological abnormalities in post-tetanic potentiation, synaptic fatigue, synaptic vesicle replenishment, and an aging-related reduction in mitochondrial complex I activity. Single-cell RNA sequencing showed that excitatory neurons exhibited an altered transcriptomic profile involving "protein translation" and "oxidative phosphorylation". DiscussionAccumulation of NFA-A{beta} alters neuronal metabolism but does not activate inflammation. Depletion of all forms of A{beta} may be required to eliminate A{beta} toxicity with anti-amyloid antibodies.

neuroscience↗

Effects of Inflammatory Factors on the Migration and Repair of Intestinal Mucosal Cells at Pancreaticojejunostomy Anastomosis: An Experimental Study in Beagle Dogs

ObjectiveTo investigate the effects of inflammatory factors on the migration and repair of intestinal mucosal cells at the site of pancreaticojejunostomy (PJ) anastomosis and to observe the safety and feasibility of PJ with mucosal-priority healing (PM-PJ). Materials and methodsThirty-six Beagle dogs were randomly divided into two groups: the PM-PJ group (n=18) and the control group (n=18), which included classic end-to-side invagination pancreaticojejunostomy (IPJ). Six Beagles were sacrificed on the 7th, 14th, and 21st days after surgery to obtain pancreaticojejunostomy anastomosis tissues. The primary outcomes were postoperative mortality, morbidity, and pathological changes in the anastomosis. The secondary outcomes were the expression levels of the cytokines TGF-{beta}1, IL-10, TNF-, IL-6, collagen, and -SMA. ResultsAll surgeries were successfully performed. In the study group, the incidences of anastomotic leakage and pancreatitis were 0% and 11.1% (2/18), respectively, whereas in the control group, the incidences were 5.6% (1/18) and 16.7% (3/18), respectively. The levels of serum TGF-{beta}1, IL-10, TNF-, and IL-6 were increased at all time points after surgery in both groups, and these increases were more significant at certain time points in the study group. Pathological observation revealed that the degree of anastomotic healing in the study group was greater than that in the control group at all time points. The protein expression levels of collagen I/III and -SMA in the anastomoses of both groups changed over time, and the changes were more significant at certain time points in the study group. ConclusionInflammatory factors play a positive role in the early stage of PJ anastomosis healing by stimulating collagen secretion and synthesis. PM-PJ is a safe and simple surgery with good anastomotic healing and a low incidence of complications.

animal behavior and cognition↗

PLXNB1 and other signaling drives a pathologic astrocyte state contributing to cognitive decline in Alzheimer's Disease

Alzheimers disease (AD) is marked by the coordinated emergence of disease-associated cell states across multiple cell types. Here, we first performed a meta-analysis of single-nucleus transcriptomic (snRNAseq) data from 869 brains of diverse decedents, confirming the critical role of an SLC38A2highSMTNhighCACNA1Dhighastrocyte subset, Astrocyte 10 (Ast10), in AD and aging-related cognitive decline. We then investigated the signaling drivers of Ast10s emergence in the aging brain, focusing on interactions among microglial and astrocytic subsets. Analysis of the snRNAseq data prioritized a set of ligands and receptors that are robustly predictive of Ast10 proportions across participants, and we confirm our predictions in multiple studies. Independent validation with spatial transcriptomics reveals striking colocalization of these prioritized ligands with the Ast10 signature in AD brain tissue, but not with other astrocytic states. Genetic ablation of a top receptor PLXNB1 in murine and human iPSC-derived astrocytes decreased the Ast10 signature, confirming its regulatory role. Finally, we find that Ast10 may contribute to cognitive decline through synaptic loss and is associated with cognitive decline independent of AD. Thus, Ast10 and its regulators are potential points of convergence for multiple neurodegenerative mechanisms and may be promising targets for therapeutic development to preserve cognitive function.

neuroscience↗

Mapping Anhedonia-Related Damage Network: Insights for TMS Treatment

BackgroundMany studies have explored anhedonia-related functional connectivity (FC), but the findings remain inconsistent. There is a gap in identifying a consistent anhedonia-related damage network and applying it to TMS treatment. MethodsWe systematically reviewed studies on anhedonia-related functional connectivity and identified anhedonia-related brain damage locations. Using a novel functional connectivity network mapping approach applied to a large normative connectome dataset, we mapped these damage locations to anhedonia-related damage networks. Subsequently, transcriptomic analysis was conducted to uncover underlying molecular mechanisms. Additionally, we investigated the application of the anhedonia-related damage network in transcranial magnetic stimulation (TMS) treatment, focusing on changes in FC within this network following TMS treatment and its association with anhedonia improvement, as well as predicting TMS treatment efficacy based on baseline FC within the anhedonia-related damage network. ResultsA total of eight experiments from seven studies using the nucleus accumbens (NAc) as the seed were eligible for functional connectivity network mapping analysis. This study identified an anhedonia-related damage network, primarily characterized by disrupted functional connectivity between the NAc and the default mode network. Transcriptomic analysis revealed gene enrichment associated with synaptic signaling, neuronal development, ion transport, and actin cytoskeleton regulation. TMS treatment increased NAc functional connectivity within the anhedonia-related damage network in the response group, with these changes correlating with improvements in anhedonia. Furthermore, baseline NAc FC within this network demonstrated predictive potential for TMS treatment efficacy. ConclusionThe anhedonia-related damage network was identified, emphasizing its underlying mechanisms and predictive value for TMS in treating anhedonia.

neuroscience↗

Cell signaling pathways discovery from multi-modal data

Deciphering cell signaling pathways is key to understanding biology, disease mechanisms, and developing new therapies. Although advances in multi-omics technologies provide richer insight into signaling, the data remain high-dimensional, heterogeneous, and difficult to interpret, and current computational tools for inferring signaling pathways are limited. To address this, we developed Incytr, a method for efficient discovery of cell signaling pathways through integration of diverse data modalities, including transcriptomics, ATAC-seq, proteomics, phosphoproteomics, and kinomics. We demonstrate its application in COVID-19, Alzheimers disease, and cancer, where it successfully recovers known pathways and generates novel, cell-type-specific hypotheses supported by multiple data types. We further show how integrating Incytr-derived pathways with biomarker and drug databases can support target and drug discovery. Finally, we show that using Incytr-derived signaling pathways as training data for simple natural language processing models can deepen our understanding of cell-cell communication and immune cell dynamics, while helping identify new therapeutic targets.

bioinformatics↗

Spatial transcriptomics reveals heterogeneous cell-cell interactions among brain regions in a cuprizone model consistent with multiple sclerosis lesions

The cuprizone (CPZ) model is widely used for modeling demyelination in multiple sclerosis (MS) and for testing potential remyelination therapies. We integrated single-cell and spatial transcriptomics (ST) to fine map the spatial cellular and molecular responses during de and remyelination. ST revealed global demyelination and neuroinflammation in the brain beyond the corpus callosum, with region-specific differences. We identified oligodendroglia and microglia as two major cell types with significant transcriptomic changes in the model. Ligand receptor pairing analyses predicted growth factor and phagocytic pathway enrichment during demyelination, which is consistent with changes in MS lesions. During remyelination, while mature oligodendrocytes nearly reversed their phenotype back to the control state, microglia remained associated with the demyelination phenotype. Finally, astrocytes in the CPZ model had the greatest preservation of disease-associated modules to MS lesions, while the MOL, OPC, and microglia showed moderate to low preservation, which overall suggested that the CPZ model had moderate translatability to chronically active MS lesions.

neuroscience↗