Background: Imatinib has been widely used in gastrointestinal stromal tumours and significantly improved the prognosis of GIST patients, but approximately half of patients develop acquired treatment resistance, highlighting the urgency for novel therapeutic strategies.

Methods: A variety of bioinformatic tools and laboratory experiments, RNA sequencing, animal models and the thermal proteome profiling assay were employed to validate our findings and investigate the antitumour effects of β-elemene.

Results: We found that imatinib-resistant GIST was associated with negative regulation of ferroptosis activity, and inducing ferroptosis can enhance the sensitivity of resistant cells to imatinib. Furthermore, we found that β-elemene enhances imatinib sensitivity in imatinib-resistant GIST cells through inducing ferroptosis. Moreover, the combination treatment of β-elemene and imatinib showed significantly increased antitumour efficacy, compared to each monotherapy, both in vitro and in vivo. Mechanistically, β-elemene specifically targets N6AMT1, inhibiting its transcriptional repression function and activating the nuclear factor erythroid 2-related factor 2 (NRF2)-HMOX1 signalling pathway to induce ferroptosis.

Conclusion: Β-elemene can target N6AMT1 and promote ferroptosis by increasing the expression of NRF2 and HMOX1. These findings suggest β-elemene as a prospective therapeutic strategy to improve the sensitivity of imatinib in gastrointestinal stromal tumours.

Background: Extrachromosomal circular DNA (eccDNA) has emerged as a critical driver of oncogenesis, yet its functional roles in high-grade serous ovarian cancer (HGSOC) remain poorly characterized. This highlights the need for comprehensive investigations into the abundance, biogenesis, and functional implications of eccDNA in HGSOC.

Methods: To characterize eccDNA in HGSOC, we performed comprehensive Circle-seq analysis to assess eccDNA abundance and genomic annotation in HGSOC tissues compared to normal ovarian tissue. For mechanistic validation of eccDNA biogenesis pathways, targeted knockdown experiments of microhomology-mediated end-joining (MMEJ) dependent on LIG3 and POLQ were conducted. Functional characterization of HGSOC-specific eccDNA-harboring precursor microRNAs (eccMIRs) included in vitro assays using HGSOC cells and in vivo tumor growth experiments.

Results: Circle-seq analysis revealed a 13-fold increase in eccDNA abundance in HGSOC compared to normal ovarian tissue, with significant enrichment in promoter and coding regions. The MMEJ pathway was identified as the predominant pathway for eccDNA biogenesis in HGSOC, supported by characteristic microhomologies at junction sites and validation via LIG3 and POLQ knockdown experiments. Notably, HGSOC-specific eccDNA frequently contained functional eccMIRs (eccMIR3661, eccMIR618, and eccMIR2277), which generate oncogenic miRNAs. These miRNAs promote tumor progression by downregulating tumor suppressor genes and activating key oncogenic pathways. Functional assays confirmed that these eccMIRs significantly enhanced HGSOC cell proliferation, migration, and invasion in vitro and promoted tumor growth in vivo.

Conclusions: These results underscore eccDNA as an oncogenic driver in HGSOC through non-coding RNA-mediated regulatory mechanisms, revealing novel therapeutic opportunities for targeting eccDNA biogenesis in this aggressive malignancy.

Background: Protein expression asymmetry between brain hemispheres is hypothesized to influence functional connectivity, yet its role in language-related networks remains poorly understood. Additionally, how such molecular differences relate to brain reorganization in glioma requires further exploration.

Methods: We performed label-free tandem mass spectrometry on 13 left-hemispheric language-related Brodmann areas (BAs) and their right-hemispheric counterparts from 10 donor brains, identifying protein signatures across 6 language-related functional modules. We then compared these proteomic profiles with resting-state structural and functional connectivity data from 26 BAs across 90 subjects from the Human Connectome Project (HCP). Finally, we examined functional compensation in 13 glioma patients with tumors in Wernicke's area, correlating gray matter volume in contralateral homologs with linguistic performance.

Results: Protein expression heterogeneity was greater within hemispheres than between homologous contralateral BAs. Hierarchical clustering revealed interactions between core language areas (Broca's, Wernicke's, Geschwind's) and auditory/motor regions. Functional connectivity strength correlated with protein expression similarity, particularly in symmetric BA4 (primary motor cortex). Excitatory/inhibitory (E/I) neuronal markers (GRIA1/GRIA4) showed a left-positive, right-negative correlation with connectivity, suggesting hemispheric differences in synaptic regulation. Glioma patients exhibited right-hemispheric compensation, with gray matter volume in Wernicke's homolog correlating with linguistic function.

Conclusion: Our findings support the hypothesis of a homophilic mixing effect between protein expression similarity and connectome architecture, and help explain brain rearrangement in glioma patients.

Background: Alveolar macrophages (AMs) are crucial innate immune cells that play important roles during infection with severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Ex vivo human precision-cut lung slices (PCLSs) are well-suited models to study immune reactions and biochemical changes within host cells as well as to follow functional macrophage phenotype plasticity within complex tissue environment. Raman spectroscopy emerged in recent years as a powerful method for label-free cell characterization.

Methods: Human PCLSs from one donor were infected with either the SARS-CoV-2 delta or omicron variant. Immunofluorescence microscopy localized AMs and virus particles. Cytokine levels of interferon-gamma (IFN-γ) and interleukin 18 (IL-18) were quantified. The lung slice model was optimized for label-free Raman spectroscopic imaging and for the characterization of single AMs within the three-dimensional structure of the PCLS model.

Results: Fluorescence microscopy confirmed the location of AMs and virus particles within the PCLS model. Raman spectroscopic imaging generated false-colour images, revealing distinct spectroscopic differences between AMs in the uninfected control PCLS model and those in PCLS models infected with SARS-CoV-2. These differences included variations in intracellular RNA, carotenoid, triacyl glyceride, and glucose levels, consistent in interpretation with cytokine quantification data. A linear discriminant analysis (LDA) classification model achieved an 83% accuracy in distinguishing cells from infected lung slices from those of the uninfected controls. The LDA loadings pointed to spectral bands that had been previously identified in an in vitro stimulation study of macrophages.

Conclusions: Raman spectroscopy can characterize the cellular immune response and phenotype plasticity of AMs to infection with SARS-CoV-2 within a PCLS model in a label-free and non-invasive manner. The ability to distinguish cells from infected PCLSs from cells of the uninfected control PCLS based on intracellular biochemical changes highlights the potential of Raman spectroscopy as a powerful diagnostic tool in immunology and clinical diagnostics.

Computational modeling and simulation are playing an increasingly important role in oncology, bridging biological research, data science and clinical practice to better understand cancer complexity and inform therapeutic development. This special issue presents recent advances in multiscale modeling, artificial intelligence-driven systems, digital twins, and in silico trials, illustrating the evolving potential of computational tools to support innovation from bench to bedside. Together, these contributions outline a future in which precision medicine, adaptive therapies and personalized diagnostics are guided by integrative and predictive modeling approaches.

Background: Tumour suppressor genes, exemplified by TP53 (encoding the human p53), function as critical guardians against tumourigenesis. Germline TP53-inactivating mutations underlie Li-Fraumeni syndrome, a hereditary cancer predisposition disorder characterised by early-onset pan-tissue malignancies. However, the context-dependent tumour-suppressive mechanisms of p53 remain incompletely elucidated. This study aims to investigate the disruption of cellular homeostasis and tumourigenic mechanisms following p53 inactivation across distinct cell lineages.

Methods: Trp53 (encoding mouse p53) knockout mouse model was employed to study molecular alterations under p53-deficient conditions. Multi-omics analyses – including single-cell transcriptomics, single-cell ATAC-seq, spatial transcriptomics, whole genome sequencing, and CUT&Tag – were integrated to construct a Trp53 functional cell landscape. Deep learning-based gene network models were employed to reconstruct p53 regulatory networks and simulate in silico perturbations caused by p53 loss.

Results: Our analyses revealed transitional dynamics in immune, stromal, and epithelial cells from normal physiology to p53-deficient states and subsequent tumourigenesis. These transitions implicated critical pathways such as cell cycle regulation, stress response, metabolic reprogramming, and immune modulation, displaying both lineage-conserved and lineage-specific features. Tumour-prone cell populations exhibiting elevated differentiation plasticity were identified across lineages within tumourigenic trajectories. Spatial transcriptomic profiling confirmed the emergence of thymic tumour-initiating T-cell clusters characterised by deterministic chromatin architectural disruptions under p53-loss pressure. Notably, we uncovered a recurrent upregulation signature of ribosomal protein genes as an early pivotal molecular event preceding malignant transformation in p53-deficient oncogenesis. Finally, we decoded the p53 downstream regulatory network and computationally evaluated the perturbation effects of genetic inactivation at single-cell resolution.

Conclusions: Our results elucidate the multiscale consequences of p53 inactivation while providing valuable resources for understanding tumour predisposition associated with p53-inactivating mutations and developing clinical interception strategies.

Background: Atg7-autophagy–related gene 7 contributes as an immune cell function regulator, particularly involved in CD4⁺ T cell response. Nevertheless, the specific contribution of Atg7 in CD4⁺ T cells sensitive immune responses in inflammatory bowel disease (IBD) remains largely unclear. This study explores the functional significance and regulatory mechanisms of CD4⁺ T cell-specific Atg7 in IBD.

Methods: Real-Time Quantitative Reverse Transcription PCR (qRT-PCR), western blotting analysis, flow cytometry and immunohistochemistry were employed to evaluate ATG7 expression in peripheral blood and colonic mucosal biopsies from IBD patients. Peripheral CD4⁺ T cells were transfected with lentivirus vectors encoding either ATG7 (LV-ATG7) or ATG7 short hairpin RNA (LV-shATG7). Furthermore, mice with a CD4⁺ T cell conditional knockout of Atg7 (Atg7^ΔCD4) were generated, and CD4⁺ T cells of splenic origin were subjected to RNA-seq.

Results: ATG7 level was markedly elevated in inflamed mucosa tissues and peripheral blood CD4⁺ T cells of patients with active Crohn's disease compared to healthy individuals. Overexpression of ATG7 suppressed Th1 differentiation while enhancing the induction of iTreg cells. Atg7^ΔCD4 mice exhibited exacerbated result of 2,4,6-trinitrobenzenesulphonic acid-induced experimental colitis, as did Rag1^−/− mice adoptively transferred with CD45^RBhigh CD4⁺ T cells from Atg7^ΔCD4 donors. RNA-seq analysis revealed that E26 transformation-specific sequence-1 (Ets1) acts downstream of Atg7 and mediates its regulatory effects on Th1 and Treg cell differentiation.

Conclusion: Our data indicate that Atg7 alleviates mucosal inflammation by modulating Th1/Treg differentiation through the regulation of Ets1 expression. Thus, CD4⁺ T cell-expressed Atg7 may serve as a promising therapeutic approach for IBD.

Background: Immunotherapy has revolutionised melanoma treatment, providing significant clinical benefits by reactivating the anti-tumour immune system. CD8⁺ tissue-resident memory T lymphocytes (CD8⁺ TRM) have emerged as crucial mediators of anti-tumour immunity, while their specific role in melanoma remains poorly understood.

Methods: Following CD8⁺CD45.1⁺ OT-1 cell adoptive transfer into CD45.2⁺ mice, we employed magnetic separation to purify and analyse resident memory CD8⁺ T cells (TRM). We use multiple immunohistochemistry (mIHC) to evaluate the spatial distribution of CD8⁺ TRM in ZS melanoma cohort. Additionally, the biological function of CD8⁺ TRM and their impact on anti-tumour immunity are explored using scRNA sequencing and spatial transcriptomics, coupled with in vivo/in vitro experiments. Finally, CD8⁺ TRM utility as an immunotherapy response predictor is examined across several independent cohorts.

Results: CD8⁺ TRM demonstrates potent tumour-killing capabilities in melanoma, with CD103 as a distinctive marker. High CD103⁺CD8⁺ TRM infiltration in tumour tissues strongly correlates with improved prognosis in melanoma patients. In vivo adoptive transfer of CD103⁺CD8⁺ TRM effectively inhibits melanoma progression. Mechanistically, CD103 activates the integrin-dependent PI3K/AKT signalling cascade, promoting both proliferation and anti-tumour effector functions of CD8⁺ TRM. Notably, CD103⁺CD8⁺ TRM preferentially localises within tertiary lymphoid structures (TLS), and its adoptive transfer promotes TLS formation. Clinically, CD103⁺CD8⁺ TRM is enriched in immunotherapy-responsive patients and serves as a strong predictor for immune checkpoint blockade (ICB) treatment outcomes.

Conclusions: CD103⁺ CD8⁺ TRM cells in melanoma play a key role in the anti-tumour immune process and can also be used as a reliable predictor of immunotherapy efficacy.

Purpose: This study aimed to characterise urinary organic acid profiles in Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency (NICCD) and develop a diagnosis model to distinguish NICCD patients from those in the non-specific metabolic abnormalities group (NAG), both of which exhibit elevated urinary 4-hydroxyphenyllactic acid (4-HPLA) and 4-hydroxyphenylpyruvic acid (4-HPPA), potentially leading to misdiagnosis.

Methods: A retrospective study was conducted from February 2021 to February 2025, enrolling 105 NICCD patients, 144 healthy controls (HC), and 298 individuals from NAG. Urine organic acids were measured using gas chromatography-mass spectrometry. Data from NICCD and NAG collected before October 2024 were used for model training and internal testing, with later data serving as an external validation. A three-step feature selection strategy identified biomarkers. Five machine learning (ML) methods were used to construct the model. Performance was compared using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, specificity, F1 score, etc.

Results: Compared to HC, NICCD patients exhibited 39 differential metabolites, enriched in tyrosine, aspartate, pyruvate, lipoic acid, and TCA cycle pathways. 4-HPLA, 4-HPPA, galactitol, 4-hydroxyphenylacetic acid, pyruvic acid, quinolinic acid, homovanillic acid, 4-hydroxybenzoic acid, and malic acid showed high diagnostic performance (AUC > .8). Nine robust markers were identified between NICCD and NAG. The random forest model demonstrated superior classification performance, with high AUC, accuracy, F1 score, and low Brier score. An online calculator was developed for clinical use.

Conclusion: Our findings highlight NICCD metabolic enrichment in energy and amino acid pathways and present an interpretable ML model for distinguishing NICCD from those of NAG.

Spatiotemporal distributions of intracellular elements (e.g., small molecules, proteins and organelles) dynamically altered in response to extracellular stimuli and pathogens, regulating those element movements, remodelling, and functions independently of mere changes in element abundance. To distinguish from conventional one- or two-dimensional spatialization, we define the precise three-dimensional localisation and interactions of intra- and extracellular elements at the single cell level as the “stereologically spatiotemporal cell” (SST-cell). For example, the three-dimensional construction of chromosomes ensures their proper formation and spatial positioning, facilitates the recruitment of regulatory factors, and underlies the mechanisms by which these factors maintain chromatin architecture. A large number of intracellular organelles and sub-organelles, along with their intercommunications, decide cellular biological types, subtype specification and type-specific functions. With the development of Stereo-Cell and Stereo-seq, the measurement of spatial SST-cell omics probably enables the detailed dissection of spatial heterogeneity among different cell subtypes and states, as well as their intercellular communications. Furthermore, the new approach of single SST-cell drug screening will be innovated for developing the new generation of clinical precision therapies.

One sentence summary: This review focusses on microbiome-derived metabolites and their role in immunometabolism and the enhancement of checkpoint inhibitor responses.

Background: To investigate the role of self-peripheral blood mesenchymal stem cell (PBMSC)-derived exosomes (Exos) in enhancing renal sympathetic denervation (RD)-mediated heart regeneration following myocardial infarction (MI) in a porcine model.

Methods: Pigs (ejection fraction [EF] < 40% post-MI) were randomised to early sham RD or RD. At 2 weeks post-MI, autologous PBMSC-Exos were collected. At 30 days post-MI, pigs received either PBMSC-Exos (2 × 10¹³ particles) or phosphate-buffered saline and were followed until 90 days. Another cohort underwent myocardial biopsy at 14 days post-MI to assess PBMSC-Exos effects on ischaemic cardiomyocyte (CM) reprogramming, followed by adeno-associated viral therapy with miR-141-200-429 sponges or negative control sponges to explore the role of miR-141-200-429 clusters in reprogramming.

Results: Two weeks post-MI, RD hearts showed increased Exos uptake and inhibited the sympathetic nervous system. By 90 days, the RD+Exos group had 11%–26% higher EF than single-treatment groups (all p < .001), with improved survival and reduced fibrosis. Exos therapy enhanced RD effects by suppressing the renin‒angiotensin‒aldosterone system and transferring the miR-141-200-429 cluster into ischaemic CMs. CMs from RD-treated hearts cocultured with PBMSC-Exos^RD exhibited a more immature state, promoting reprogramming. β-Catenin overexpression further enhanced PBMSC-Exos^RD effects, while miR-141-200-429 inhibition blocked RD-induced CM reprogramming and survival. Ultimately, PBMSC-Exos^RD reduced dickkopf-1 (Dkk1) expression and activated GSK3β phosphorylation, thereby stimulating the Wnt/β-catenin pathway.

Conclusions: PBMSC-Exos^RD enhances RD-mediated cardiac repair through miR-141-200-429 cluster-dependent activation of the Wnt/β-catenin pathway, offering a novel therapeutic strategy for MI-induced heart failure. Our findings unveil a novel therapeutic strategy, highlighting that RD maintains its efficacy and safety when integrated with complementary approaches over extended periods.

Stereo-cell is a newly developed platform for spatial single-cell sequencing that integrates morphology, transcriptomics, and proteomics in high resolution. By preserving spatial context while enabling multimodal profiling, it bridges the gap between advanced omics and traditional pathology, supporting the detection of rare cells and clinically interpretable diagnoses. This letter highlights the technical innovations of Stereo-cell, its positioning within the spatial omics landscape, and its potential for precision medicine. Important challenges in data integration, regulatory compliance, and digital modelling are discussed as essential steps on the path to clinical implementation.