Biology subjects

Hu, X.

Publications and source records attributed to Hu, X..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Germline-targeting HIV Envelope SOSIP immunization more frequently elicits broadly-neutralizing antibody precursor responses in infant compared to juvenile rhesus macaques

A vaccine capable of inducing broadly neutralizing antibodies (bnAbs) is essential for effective prevention against HIV in children and adolescents. Germline-targeting vaccine strategies aim to stimulate bnAb precursor B cells through carefully designed immunogens, such as the stabilized SOSIP trimers, which mimic native HIV envelope (Env) proteins while presenting key neutralizing epitopes to germline B cell receptors. Given the ability of children living with HIV to develop bnAbs earlier and at a higher frequency than adults, we compared the immunogenicity of a CD4 binding site (CD4bs) bnAb germline-targeting SOSIP trimer immunization strategy in infant (n = 5) and juvenile (n = 4) rhesus macaques (RMs). Animals received 3 doses of the germline-targeting BG505 GT1.1 immunogen, followed by 3 boosts of wild-type BG505 SOSIP, each adjuvanted with the TLR7/8 agonist, 3M-052-SE. After 1.5 years, the RMs were further boosted with a mixed clade B Env trimer nanoparticle to enhance heterologous virus neutralization responses. This germline-targeting strategy induced equivalent titers of neutralizing antibodies in both groups of RMs, yet the infants exhibited a higher magnitude of vaccine-specific IgG binding. Notably, after 3 doses of BG505 GT1.1 SOSIP, infants had higher BG505 GT1.1-specific IgD- B cells. Upon completion of the vaccine regimen, 4 of 5 infants developed a CD4bs bnAb precursor response detectable in serum compared to only 1 of 4 juveniles. Finally, administration of the mixed clade B nanoparticle was able to increase the breadth of antibody responses in 3 of 5 infants and 2 of 4 juveniles. These results suggest that immunization in early-life may enhance bnAb induction and highlight the potential for future pediatric HIV-1 vaccine strategies. Author SummaryVaccines that can generate antibody responses that have breadth and potency in neutralization can protect children and adolescents from acquiring multi-strain viruses like HIV. Increasingly, vaccine strategies have become better tailored to elicit these broadly neutralizing antibodies (bnAbs), such as the germline-targeting HIV envelope antigens, which have shown great promise. To determine if we could elicit protective antibody responses against HIV in early life, we immunized infant and juvenile monkeys using the same vaccine strategy. In this study, we found that while both infants and juveniles developed similar levels of antibodies that could neutralize HIV, the infants showed stronger antibody responses in several key areas. Moreso, infants developed the type of early antibody response that researchers believe is needed to eventually evolve into broadly neutralizing antibodies. These findings suggest that initiating HIV vaccination earlier in life may offer a better chance at generating the bnAbs needed to protect against various HIV strains. Our work highlights the potential benefits of initiating an HIV vaccine regimen in childhood.

immunology↗

bioRxiv2025

Transposable elements drive species-specific and tissue-specific transcriptomes in human development

BackgroundTransposable elements (TEs) are an abundant and crucial regulatory resource in the human genome. Serving as alternative promoters, TEs can be reactivated and produce TE-initiated transcripts, which play importance roles in early development and differentiated tissues. However, the prevalence and function of TE-initiated transcription in human development are poorly characterized. ResultsWe identified 12,918 TE-initiated transcripts across 40 human body sites and embryonic stem cells. Among TE-initiated transcripts, 80% were activated in a tissue-specific manner. TEs with tissue-specific transcription factor binding motifs were enriched in particular tissues. Additionally, approximately half of TE-derived TSSs were primates-specific. Notably, 375 primates-specific TE-derived TSSs were found to create novel tissue-specific gene expression patterns during evolution. ConclusionsOur results characterize the global profile of TE-initiated transcription and enhance our understanding of TE contribution to the primate-specific gene regulatory networks in human development.

bioinformatics↗

bioRxiv2025

TEITbase: a database for transposable element (TE)-initiated transcripts in human cancers

Transposable elements (TEs) are abundant and play a crucial regulatory role in the human genome. Functioning as alternative promoters, TEs can be reactivated to produce TE-initiated transcripts. In cancer, TE-initiated transcription may upregulate oncogene expression and generate novel tumor-specific antigens, which could serve as potential targets for immunotherapy. However, there remains a lack of comprehensive databases that systematically investigate TE-initiated transcription in cancer. To address this gap, we developed a deep learning-based method and identified 38,995 TE-initiated transcripts across 33 cancer types from The Cancer Genome Atlas. Among these, 6,203 were tumor-specific expressed and strongly associated with the tumorigenesis. Using these annotations, we created TEITbase (http://teitbase.medbioinfo.org/), a user-friendly database that provides researchers with tools to conduct various downstream analyses and investigations for TE-initiated transcripts, including 546 novel onco-exaptation events. The establishment of TEITbase provides new insights into transcriptional reprogramming in cancers and enables further investigation into the potential roles of TE-initiated transcripts in cancer diagnostics and therapeutic strategies.

bioinformatics↗

bioRxiv2025

Neuropeptide signalling and perineurial barrier generate a persistent stress-induced internal state in Drosophila

Although fear conditioning has elucidated cue-evoked acute fear responses, the mechanisms by which stress experiences induce generalized internal states linked to anxiety are poorly understood. Here, we report that robust stress induces a persistent behavioral change characterized by avoidance of a confined space, claustrophobia-like behavior in Drosophila. Unlike aversive memory formation, the development of claustrophobia-like behavior does not require dopamine receptors. Our neuronal screening determined that neuropeptide signalling via Allatostatin-A inactivates the downstream neurons via its receptor AstA-R1, causally inducing claustrophobia-like behavior. Moreover, gene expression profiling of individual fly heads revealed that immune response activation in perineurial barrier is involved in claustrophobia-like behavior. Our data demonstrate that stress-induced persistent behavioral change would not be related to a canonical mechanism of aversive memory formation, rather involves neuropeptidergic signalling and perineurial barrier, providing the mechanism determining internal states which persistently change behavioral modes.

neuroscience↗

bioRxiv2025

Design of peptide-based PAC1 antagonists combining molecular dynamics simulations and a biologically relevant cell-based assay

The PACAP receptor PAC1 is a Gs-coupled family B1 GPCR for which the highest-affinity endogenous peptide ligands are the pituitary adenylate cyclase-activating peptides PACAP38 and PACAP27, and whose most abundant endogenous ligand is PACAP38. PACAP action at PAC1 is implicated in neuropsychiatric disorders, atherosclerosis, pain chronification, and protection from neurodegeneration and ischemia. As PACAP also interacts with two related receptors, VPAC1 and VPAC2, highly selective ligands, both agonists and antagonists, for PAC1 have been sought. To date, the peptide PACAP(6-38) and polypeptide M65, which is related to maxadilan, a sandfly vasodilator peptide, have been identified as selective for PAC1. Several non-peptide small molecule compounds (SMOLs) have been reported to be specific antagonists at PAC1, albeit their specificities have not been rigorously documented. Here, we present a platform of cellular assays for the screening of biologically relevant antagonists at PAC1 and show that some currently proposed SMOL antagonists do not have activity in this cell reporter assay, while we confirm that PACAP(6-38) and M65 are competitive antagonists. We have used this assay system to explore other peptide antagonists at PAC1, guided by molecular dynamics analysis of the PACAP-PAC1 interaction based on cryo-EM structural models of PAC1 complexed with a number of biologically active ligands. The affinity-trap model for the PAC1-ligand interaction successfully predicts the engagement behavior of PACAP27 and PACAP38 peptide-based PAC1 inhibitors. In particular, C-terminal deletants of PACAP(6-38) that maintain equipotency to PACAP(6-38) allow the shorter sequence to function as a scaffold for further peptide-based antagonist exploration.

pharmacology and toxicology↗

bioRxiv2025

Manganese suppresses tumor growth through hyper-activating IRE1α

IRE1 and its downstream XBP1 signal is the most conserved unfolded protein response pathway that cells utilize to combat endoplasmic reticulum stress, also known to be utilized by tumor cells to adapt to harsh environment, leading to tumor progression. Several inhibitors against IRE1 have been developed, some of which show promising effect in clinical trial for cancer therapy, but none of them have been used in practice. Considering that hyper-activation of IRE1 induces cell death, we hypothesize that activation of IRE1 could be an alternative way for tumor suppression. Here, we identified divalent manganese ion as a potent activator to IRE1, which interacts with the cytosolic part of IRE1 directly, augmenting the downstream pro-apoptotic pathway but not the pro-survival outcome. Mn2+ limits tumor growth in xenograft model in an IRE1-dependent way. Our finding suggests pharmacological activation of IRE1 as an underestimated but promising way in cancer therapy. HighlightsO_LIMn2+ binds to cytosolic segment of IRE1 and promotes its oligomerization C_LIO_LIMn2+ hyper-activates IRE1 and induces downstream terminal UPR under ER stress C_LIO_LIMn2+ does not elevate XBP1s expression C_LIO_LIMn2+ as an IRE1 activator impairs tumor growth in xenograft model C_LI

cancer biology↗

bioRxiv2025

Characterization of MEK1/2 Degraders Uncovers a Kinase-Independent Role for MEK1/2 in the Stabilization and Maturation of CRAF

Altered MAPK signaling frequently occurs in human disease. MEK1 and MEK2 (MEK1/2) are central protein kinases in the MAPK signaling cascade that phosphorylate ERK1/2 promoting cell growth. MEK1/2 degraders offer a strategy to characterize both kinase-dependent and independent functions of MEK1/2. Here, we discovered that MEK1/2 degradation, but not kinase inhibition, caused the subsequent degradation of upstream kinase CRAF via a cell-intrinsic mechanism. MEK1/2 binding to CRAF, but not MEK1/2 catalytic activity, was required for CRAF protein stability and maturation to a functional kinase. In the absence of MEK1/2, a minor pool of newly synthesized immature CRAF that had anti-apoptotic functions remained. Finally, we showed that a stable primed CRAF-MEK1/2 signaling complex existed in cells that required RAS binding to potentiate MEK-ERK phosphorylation. Together, weve discovered a previously unrecognized kinase-independent function of MEK1/2, while contextualizing MEK1/2 as an integral component of the CRAF activation cycle beyond the conventional CRAF-MEK kinase- substrate paradigm.

cancer biology↗

bioRxiv2025

Lipocalins are versatile regulators of development and stress response in mosses

Major physiological and developmental innovations, such as stress tolerance strategies and three-dimensional growth, are key to land plant adaptation and evolution, but their genetic basis remains to be fully understood. Although lipocalins are known for their role to optimize adaptation and development in animals, they are heavily understudied in plants. Here we show that lipocalins in the moss Physcomitrium patens are versatile regulators of miscellaneous key physiological and developmental processes. Phylogenetics analyses revealed three major groups of plant lipocalins, including a newly identified group that is restricted to seedless plants. The temperature-induced lipocalin gene in P. patens (PpTIL) is functionally conserved with flowering plants in response to various abiotic stresses (e.g., heat, cold, salt, and dehydration). We demonstrate that PpTIL not only regulates protonemal development and the transition from two-dimensional to three-dimensional growth, but also affects many other processes such as lipid transport and metabolism, auxin biosynthesis and transport, and chlorophyll catabolism. These findings provide major insights into the role of lipocalins in land plant evolution.

evolutionary biology↗

bioRxiv2025

How sleeping minds decide: state-specific reconfigurations of lexical decision-making

Decision-making is a core cognitive function that enables adaptive behavior across diverse contexts. While extensively studied in wakefulness, its persistence and reconfiguration across sleep states remain poorly understood. Here, we use computational modeling to examine lexical decision-making across wakefulness, N1 sleep, and lucid REM sleep in both healthy participants (HP) and participants with narcolepsy (NP). Using facial electromyography (EMG) to capture real-time behavioral responses to spoken words and pseudowords during sleep, we quantify how decision-making strategies adapt under different sleep and consciousness states. Our findings reveal two key insights. First, decision-making mechanisms are dynamically reconfigured across sleep states. In N1 sleep, the advantage for word (vs. pseudoword) judgments is supported by faster sensory encoding and motor preparation, combined with efficient evidence accumulation. In contrast, in lucid REM sleep, the word advantage is driven exclusively by enhanced evidence accumulation, while sensory encoding and motor preparation remain unchanged. Second, cross-state comparisons reveal distinct patterns of preservation and impairment. In N1 sleep, word judgment remains largely intact, whereas pseudoword judgment is significantly impaired, characterized by prolonged stimulus encoding, delayed motor preparation, and reduced evidence accumulation. In contrast, lucid REM sleep is marked by a global reduction in processing efficiency, reflected in slower evidence accumulation and elevated decision thresholds for both words and pseudowords. These results demonstrate that rather than being uniformly degraded, decision-making is dynamically reconfigured across sleep stages, reflecting adaptive neurocognitive strategies that sustain cognition in altered states of consciousness. By identifying state-specific computational mechanisms, this study provides new insights into the brains resilience and flexibility under changing cognitive and physiological conditions.

neuroscience↗

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

Dynamic fingerprinting of the human functional connectome

Resting-state functional connectivity (FC) have distinct, personalized patterns that could serve as a unique fingerprint of each individuals brain. While previous brain fingerprinting methods have used functional connectivity maps over a scanning session (static method), it has been shown that the brain is a dynamic system that switches between several metastable states, each of which having a different FC map. Taking the dynamic nature of brain connectivity into account will likely lead to more subject-specific information and better individual identification. In this paper, we derived the state-specific FCs using sliding window correlation and clustering and evaluated their performance in individual identification and cognitive score prediction. The resultant dynamic fingerprints outperformed the static fingerprints in identification accuracy. Furthermore, some of the brain states were more accurate in predicting cognitive scores, indicating that connectivity in some brain states is informative of cognition abilities, possibly useful as biomarkers for brain disorders. Impact StatementOur findings suggest that state-specific functional connectivity patterns of the brain are unique for each individual. These brain states predicted participants cognitive performance, suggesting that they have the potential to be used as biomarkers for cognitive function or neurological disorders. Integrating state-based functional connectivity into clinical frameworks could potentially enhance early diagnosis and patient stratification, and lead to targeted interventions for neuropsychiatric and neurodegenerative conditions.

neuroscience↗

bioRxiv2025

Application and mechanism of anticancer peptides in organoid models of intrahepatic cholangiocarcinoma

BackgroundThe clinical manifestations of intrahepatic cholangiocarcinoma (ICC) are non-specific, and only a small number of patients are eligible for surgical resection at the time of diagnosis, limiting treatment options. Anticancer peptides (ACPs) exhibit strong inhibitory activity against tumour cell lines, exhibit minimal side effects, are easily modified and optimised, and have low production costs. These attributes make ACPs a prospect for clinical applications. Simultaneously, the development of patient-derived three-dimensional organoids as a novel disease model has enabled the replication of the structure and heterogeneity of solid tumours. These organoids provide valuable tools for understanding disease mechanisms, conducting drug sensitivity tests, and developing targeted therapies. However, the effect of ACPs at the organoid level in ICC remains unknown. Therefore, this study aims to explore the potential of ACPs in treating ICC using patient-derived organoids as a model system to evaluate their efficacy and optimize therapeutic strategies. MethodsWe designed and synthesised a novel ACP sequence and applied it to a patient-derived organoids (PDOs) model. Organoids were evaluated using histochemistry analysis and whole-exome sequencing. ACPs were compared with representative chemotherapeutic drugs, including sorafenib and gemcitabine, to assess treatment differences. Additionally, scanning electron microscopy and flow cytometry were performed for further mechanistic analyses. ResultsOrganoid models exhibited histological characteristics similar to those of maternal tumours, especially showing strong positivity for EpCAM and KRT19 expression. Furthermore, whole-exome sequencing of the primary tumour and derived organoids revealed that PDOs closely recapitulated the genomic similarities of the primary tumour across multiple levels. Drug response analyses revealed that ACPs exhibited highly efficient anti-tumour effects, with specific differences observed between patients. ACPs affected the growth of tumour cells and exerted anticancer effects through direct membrane disruption and indirect induction of apoptosis. ConclusionIn this study, organoids derived from patients with ICC were established. This in vitro model provides valuable tools for evaluating the therapeutic response of ACPs and offers novel insight for the study of ICC.

cancer biology↗

bioRxiv2025

Lemur: A Single-Cell Foundation Model with Fine-Tuning-Free Hierarchical Cell-Type Generation for Drosophila melanogaster

Single-cell genomics has revolutionized our understanding of cellular heterogeneity, but automating its analysis remains an open challenge. Cell-type annotation represents a critical bottleneck, particularly as datasets grow in size and complexity. While foundation models have shown promise in addressing this challenge, existing approaches require extensive fine-tuning for effective cell-type annotation. Here, we present Lemur (Large Expression Model for Understanding scRNA-seq), a single-cell foundation model specifically designed for Drosophila melanogaster. Lemur achieves fine-tuning-free cell-type annotation through comprehensive pre-training on an integrated whole-organism atlas with a unified cell-type annotation schema. To leverage this unified schema, we developed a dedicated hierarchical cell-type decoder architecture. This approach enables Lemur to generate consistent cell-type predictions across multiple levels of granularity without requiring additional training on new datasets. The model demonstrates strong performance across diverse tissue types, experimental conditions, and sequencing technologies. It also achieves batch-effect correction without explicitly training for this task. This automated analysis capability positions Lemur as an effective tool for the fly research community. Beyond its immediate applications, Lemur establishes a framework for accelerating biological discovery. It enables rapid iteration between computational predictions and experimental validation in the highly controlled Drosophila melanogaster system, with potential implications for translational research in human biology, particularly in aging and neurodegenerative disease studies.

bioinformatics↗

bioRxiv2025

Intense oocyte competition builds the female reproductive reserve in mice

During the process of ovariogenesis, more than two-thirds of germ cells are sacrificed to enhance the quality of the remaining oocytes. But the detail process of selection is not completely understood in mammals. Here, by creating a high resolution 4- dimensional ovariogenesis imaging system, we recorded the progress of oocyte fate determination in live mouse ovaries, and discovered an oocyte competition mechanism that determines the survival of oocytes. We found that dominant oocytes catch and absorb the cell debris from sacrificed oocytes to enrich their cytoplasm for survival. Single-cell sequencing demonstrated that this competition follows a classic autophagy- driven model. Blocking competition by suppressing autophagy resulted in an enlarged pool of survived oocytes. However, these oocytes lacking competition were unable to fully develop and contribute to fertility. Our study suggests that mammals have evolved a unique intensive competition system to enhance oocyte quality, necessary to support their long reproductive lifespan.

developmental biology↗

bioRxiv2025

Candidate transmission survival genome of Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb), a leading cause of death from infection, completes its life cycle entirely in humans except for transmission through the air. To begin to understand how Mtb survives aerosolization, we mimicked liquid and atmospheric conditions experienced by Mtb before and after exhalation using a model aerosol fluid (MAF) based on the water-soluble, lipidic and cellular constituents of necrotic tuberculosis lesions. MAF induced drug tolerance in Mtb, remodeled its transcriptome and protected Mtb from dying in microdroplets desiccating in air. Yet survival was not passive: Mtb appeared to rely on hundreds of genes to survive conditions associated with transmission. Essential genes subserving proteostasis offered most protection. A large number of conventionally nonessential genes appeared to contribute as well, including genes encoding proteins that resemble anti-desiccants. The candidate transmission survival genome of Mtb may offer opportunities to reduce transmission of tuberculosis. Significance StatementMycobacterium tuberculosis (Mtb) travels from the lungs of one person through the air to the lungs of another and survives multiple stresses en route, including changes in temperature and in concentrations of oxygen, carbon dioxide, hydrogen ions, salts and organic solutes. Here we present a genetically tractable model of transmission to begin the identification of the transmission survival genome of Mtb. We devised a fluid that mimics TB lesions, found that it protects Mtb from transmission-related stresses, associated this with the structure of the droplets as they dry and their ability to retain water, and used it to query the potential contribution of each of Mtbs genes to Mtbs survival in models of three sequential stages of transmission.

microbiology↗

bioRxiv2025

Human hippocampal ripples predict the alignment of experience to a grid-like schema

Humans create internal cognitive maps that allow us to make inferences beyond direct experience. These maps often rely on hexagonal grid-cell-like neural codes, serving as a schema for two-dimensional (2D) spaces. Yet it remains unclear how new experiences become aligned with this schema, especially in non-spatial contexts. Here, we show that hippocampal ripples - brief bursts of neuronal activity during rest - predict the emergence of grid-like codes in a novel 2D inference task. We recorded intracranial neuronal activity in 42 epilepsy patients as they learned rank relationships among feature objects (for example, objects differing in "magic" or "speed"). After learning, these objects were combined to form "compounds" occupying a 2D conceptual space defined by two feature dimensions. During learning, hippocampal ripple activity increased during pauses between trials, suggesting that ripples integrated newly acquired information offline. Subsequently, ripple activity during post-learning rest predicted the later emergence of grid-like codes in the entorhinal cortex (EC) and medial prefrontal cortex (mPFC), a core region of the default mode network (DMN), when participants inferred unseen relationships among the compounds. Critically, coordination during rest between hippocampal ripples and DMN activity in the mPFC predicted participants ability to infer complex relationships beyond direct memory retrieval. These findings provide the first direct evidence that hippocampal ripples, working with the DMN, align new experiences with a grid-like schema offline, transforming discrete learning events into structured knowledge that supports flexible and adaptive reasoning in human cognition.

neuroscience↗

bioRxiv2025

Synergizing Network Pharmacology and Pan-Cancer Analysis in TCM Repositioning for Tumor Therapy

BackgroundRepositioning Traditional Chinese Medicine (TCM) for cancer treatment, addressing heterogeneity through synergistic effects, aligns with the evolving trend of combination therapy. However, the complexity of TCM and the lack of methodology hinders the elucidation of TCM treatment mechanisms and potential indications. The research aims to construct develop a comprehensive method combining network pharmacology and pan-cancer analysis (NetPharm-PanCan) for TCM repositioning, exemplified by the Astragali Radix-Curcumae Rhizoma (ARCR) herb pair. MethodThe TCM-component-gene network was constructed using Cytoscape3.7.2 with gene screening based on components from TCMSP and targets predicted via the Swiss Target Prediction database. The core gene set of the ARCR (CGSARCR) was identified by analyzing network via the dual algorithm, namely Degree and MCODE followed by GO and KEGG enrichment analyses. The pan-cancer analysis encompassing Gene Set Variation Analysis (GSVA), immune infiltration correlation, cancer pathway analysis, and Gene Set Enrichment Analysis (GSEA) was unveiled to identify the potential indications. Multivariate cox regression analysis was employed for identifying prognostic genes, followed by the modeling for potential therapeutic indications using the R software. The Metescape database was harnessed to reveal similarities and differences in the mechanisms for prognostic genes associated with potential indications. The XGBoost algorithm was used to construct an indication prediction system according to the analysis results above. ResultThe CGSARCR comprises 28 genes targeting all ARCR components. The pan-cancer analysis revealed that the CGSARCR showed significantly higher tumor scores than normal tissue scores across nine different types of cancer, including THCA, KIRC, LUAD, COAD, BRCA, STAD, ESCA, and others. The CGSARCR correlated strongly with cancer-related pathways and the immune microenvironment. Prognostic models evaluate the potential of these indications as follows: THCA> KIRC> LUAD> COAD> BRCA> STAD> ESCA, with enrichment analysis suggesting KIRC and LUAD as the most potential indications of ARCR. The XGBoost-based system achieved high predictive accuracy (training AUC: 0.985, testing AUC: 0.96, training logloss: 0.21, testing logloss: 0.25). ConclusionThe NetPharm-PanCan method provides a robust, network-based pan-cancer analysis framework for TCM repositioning in cancer research. It provides theoretical foundations and practical tools for TCM-based drug development, with potential applicability to broader drug repurposing efforts.

bioinformatics↗

bioRxiv2024

Comprehensive analysis of macrophages infected with avirulent and virulent Mycobacterium tuberculosis uncovers distinct immune mechanisms and anti-TB effect of treated exosomes

Tuberculosis (TB) is now the worlds second deadliest infectious killer after COVID-19. Human-macrophages and their secreted exosomes play important roles in combating invading Mtb. However, the panoramic analysis of the underlying immune mechanism for the infected macrophages, package or secretion mechanism, and anti-TB effect of Mtb treated exosomes remain poorly understood. Here we conducted comprehensive analyses of the macrophages infected with avirulent and virulent Mtb (H37Ra & H37Rv) and their secreted exosomes, collected cells and corresponding exosomes for omics and phenotypic analysis. The results showed that avirulent Mtb stimulated robust immune-responses and apoptosis in macrophages to eliminate the invading Mtb; virulent Mtb induced severe necrosis and immune-escape for survival. The HMGB1 signaling pathway and TNFRSF1B plays important roles in the immune escape of virulent Mtb. Interestingly, our results suggest that macrophages kill Mtb in an IFN-{gamma} independent but simulative way, highlighting the central role of IFN signaling pathway in anti-TB immune response. Moreover, we observed selective transport of host and Mtb RNAs from macrophages to exosomes. Notably, "H37Ra-treated exosomes" displayed a higher anti-TB effect than "H37Rv-treated exosomes" due to some enriched pro-inflammation and immune-escape related Mtb proteins in these two exosomes, respectively. Conclusively, our findings shed new light on the immune mechanism of macrophages in response to Mtb infection, offering a new TB-treatment strategy and some promising vaccine candidates.

bioinformatics↗