Abstract Background Breast cancer imaging frequently combines ultrasonography (US), digital mammography (DM) and digital breast tomosynthesis (DBT), yet integrating complementary findings remains labor-intensive. Methods We developed a parallel-branch deep learning framework for breast-level risk classification from paired US, DM and DBT examinations. The models were trained on 2,187 breasts and evaluated in an internal validation cohort of 632 breasts and an independent pathology-confirmed cohort of 500 breasts. Six single- and dual-modality models were compared. Results In the internal validation cohort, US–DBT achieved the highest observed AUC of 0.944 (95% CI, 0.926–0.963), exceeding US–DM and DM–DBT but not US; its sensitivity was 0.860 (95% CI, 0.805–0.904) and specificity was 0.904 (95% CI, 0.871–0.930). In the pathology-confirmed cohort, US–DBT achieved an AUC of 0.934 (95% CI, 0.913–0.955), exceeding US and DM–DBT but not US–DM. Its specificity was higher than that of all three models (0.955; 95% CI, 0.927–0.975; all adjusted P < 0.001), with a PPV of 0.958 (95% CI, 0.931–0.977) and sensitivity of 0.850 (95% CI, 0.807–0.887), which did not differ significantly from any of the three models. Performance remained favorable in dense breasts, lesions <2 cm and lower-suspicion BI-RADS strata. Conclusions These findings identify improved specificity as the principal added value of US–DBT and support its potential use as an adjunctive breast-level tool for refining positive imaging findings and prioritizing further diagnostic evaluation. Prospective validation in representative screening populations is required.
Natural killer (NK) cells, a pivotal component of the innate immune system, exert indispensable roles in antiviral immunity by directly eliminating virus-infected cells and modulating adaptive immune responses. This review systematically synthesizes the biological characteristics of NK cells and their multifaceted functions against viral infections. The bidirectional crosstalk between NK cells and viruses is elucidated, with a focus on NK cell adaptive features and viral evasion strategies during specific viral infections. Furthermore, potential therapeutic targets and cutting-edge immunotherapeutic strategies due to modulation of NK cell activities are summarized, including monoclonal antibodies, chimeric antigen receptor-modified NK cells, and adjuvant therapy with Chinese herbal medicines. Recent clinical evidence and preclinical advances are integrated to provide a comprehensive framework for understanding NK cell-mediated antiviral immunity, identifying novel insights to guide the development of precise, effective immunotherapies for combating refractory viral infections.
mRNA therapeutics are transitioning from transient anti-viral vaccines into precise cancer immunotherapies capable of orchestrating potent antigen-specific T-cell and humoral responses. However, therapeutic resistance within immunologically "cold" tumors remains a formidable barrier, necessitating multiaxial optimization across transcript architecture, neoantigen selection, delivery vector engineering, and tumor microenvironment (TME) reprogramming. This review synthesizes critical breakthroughs in mRNA biochemistry-including chemical nucleotide modifications, optimized untranslated regions, structural codon adjustments, and stringent purification methodologies-that extend transcript longevity while limiting off-target reactogenicity to maximize functional antigen expression. We evaluate multiomic neoantigen discovery workflows leveraging genomics, transcriptomics, immunoproteomics, and computational HLA-binding algorithms to refine patient-specific target selection. Next, we dissect advanced lipid nanoparticles, surface-functionalized biomaterials, and engineered extracellular vesicles optimized to enhance antigen-presenting cell tropism and lymphoid homing. We further detail how vaccine-induced cytokine fluxes actively remodel the TME, successfully reversing local immune tolerance and driving robust effector leukocyte infiltration into the tumor stroma. Specifically, we highlight the convergence of mRNA-mediated cytokine signaling and epigenetic imprinting, which cooperatively induce trained immunity for durable preventive surveillance. Finally, we delineate rational combinations with immune checkpoint blockades while addressing translational challenges: identifying predictive biomarkers, mapping presentation kinetics, and structuring adaptive clinical trial frameworks.
Objective:To investigate the anti-inflammatory mechanisms of Hudi enteric-coated capsule (HDEC) and its major bioactive constituent, polydatin, in ulcerative colitis (UC). Methods:Mouse models of colitis were established by transplantation adoptive transfer of CD45RBhighCD4+ T cells and treated with or without HDEC/polydatin. Therapeutic efficacy was evaluated by assessing disease activity, colon length, and histopathological damage. The differentiation of Th1, Th17, and Treg cells was analyzed using quantitative real-time polymerase chain reaction and flow cytometry. In vitro cultures of mouse and human CD4+ T cells were utilized to assess the immunomodulatory activity. RNA sequencing, Western blotting, and immunofluorescence were used to explore the underlying mechanism. Molecular docking, molecular dynamics, and surface plasmon resonance (SPR) assays were employed to confirm the interaction between polydatin and KEAP1. Results:Treatment with HDEC and polydatin significantly ameliorated murine colitis and mucosal damage. Mechanistically, polydatin directly binds to KEAP1 to promote NFE2L2 nuclear translocation. This NFE2L2 activation reduces intracellular oxidative stress, thereby inhibiting pathogenic Th1/Th17 differentiation and enhancing Treg generation. Importantly, these effects were consistently validated in human CD4+ T cells and UC mucosal tissues. Conclusion:HDEC and polydatin alleviate UC by targeting the KEAP1-NFE2L2 axis to reduce oxidative stress, thereby restoring the Th1/Th17/Treg balance. This highlights polydatin as a promising KEAP1-targeting agent with strong translational potential.
Chimeric antigen receptor (CAR)-engineered immune cells have revolutionized cancer immunotherapy, expanding from the established success of CAR-T cells to a diverse array of cellular platforms. While seven FDA-approved CAR-T cell products demonstrate unprecedented efficacy in hematologic malignancies, significant limitations persist, including severe inflammatory toxicities, resistance in solid tumors, and manufacturing barriers. These challenges have catalyzed extensive research to extend CAR engineering into alternative effector cell types, such as unconventional T cell subsets, natural killer (NK) cells, macrophages, neutrophils, and dendritic cells, as well as non-immune platforms. Each cell type exhibits distinct antitumor mechanisms, persistence profiles, safety characteristics, and manufacturing requirements, positioning them to address complementary therapeutic needs. This review provides a comprehensive overview of diverse CAR-engineered cellular platforms, encompassing their biological properties, advantages, sourcing strategies, and manufacturing processes, alongside current clinical progress and optimization approaches. Beyond oncology, these platforms have demonstrated significant potential in treating autoimmune diseases, infections, cardiac fibrosis, and senescence-associated disorders. By leveraging distinct immune and non-immune cell types to mediate cytotoxicity or suppress pathogenic cells, CAR technology provides versatile therapeutic avenues across varied disease contexts. Through synthesis of recent advances in CAR platform diversity, this review identifies opportunities for targeted optimization and explores future directions for broadening CAR-based therapeutic applications.
Minor glomerular abnormalities (MGAs) are histopathologically heterogeneous renal lesions with subtle structural changes and latent clinical manifestations, yet their molecular mechanisms remain poorly characterized and underexplored. In this study, we employed PCT-assisted sample preparation combined with DIA-MS to systematically compare the proteomic profiles of distant non-neoplastic tissues (DNTs, n = 24) and MGA tissues (n = 27). A total of 9,529 protein groups were quantified with a FDR < 1%, and 1,338 differentially expressed protein groups were identified (FC > 2 or < 0.5, P < 0.05), including 190 downregulated and 1,148 upregulated PGs in MGA tissues. GO analysis revealed that the downregulated proteins were enriched in cell adhesion, ion binding, and molecular transport, whereas the upregulated proteins were enriched in transcriptional regulation, DNA replication/repair, and nucleic acid binding. KEGG pathway analysis indicated that inhibition of metabolic pathways and PPAR signaling pathway, as well as the activation of basal transcription factors and nucleotide excision repair in MGAs. Further screening revealed 13 core upregulated nuclear proteins (e.g., YY1, TAF9, RFC1, and POLR1D) with an over 90% detection rate in MGA tissues; these proteins are functionally associated with renal inflammation, cell proliferation, and the DNA damage response. Our study establishes a high-resolution proteomic landscape of MGAs, provides novel insights into their molecular pathogenesis, and identifies potential tissue biomarkers and therapeutic targets. The PCT-assisted DIA workflow also offers a robust technical framework for proteomic analysis of microscale renal biopsy samples.
Background:Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract and is mainly driven by activating KIT or PDGFRA mutations. Although tyrosine kinase inhibitors (TKIs) improve outcomes, primary and acquired resistance remain major challenges, especially in high-risk and wild-type GIST. Protein O-linked N-acetylgalactosamine (O-GalNAc) glycosylation regulates protein stability and signaling, but its role in GIST remains unclear. Methods:Bulk RNA-seq, proteomic, and single-cell RNA-seq data were integrated to identify O-glycosylation-related programs and key glycosyltransferases in GIST. Functional assays in GIST-T1 and GIST-882 cells, together with xenograft models, were performed to assess the effects of GalNAc-transferase 7 (GALNT7). GALNT7-KIT interaction, KIT O-GalNAcylation, and protein stability were examined by co-immunoprecipitation, VVA lectin blotting, confocal microscopy, and cycloheximide chase assays. Benzyl-α-GalNAc was evaluated as an O-glycosylation-targeting strategy in vitro and in vivo. Results:O-glycosylation signatures were enriched in high-risk GIST and correlated with pathological risk. High O-glycosylation scores co-segregated with elevated copy-number variation in a fibroblast-like malignant cell population. GALNT7 was identified as a hub gene, upregulated in GIST, and associated with poor progression-free survival. GALNT7 promoted GIST cell growth, migration, and xenograft formation. Mechanistically, GALNT7 interacted with KIT, catalyzed its Tn-antigen O-GalNAcylation, increased KIT protein stability, and sustained PI3K/AKT and MAPK/ERK1/2 signaling. Benzyl-α-GalNAc reduced KIT O-GalNAcylation and stability, attenuated GALNT7-driven phenotypes, and inhibited xenograft growth. Conclusions:GALNT7-mediated O-GalNAc glycosylation stabilizes KIT and drives GIST progression. GALNT7 may serve as a prognostic biomarker and therapeutic target in GIST.
Protein post-translational modifications (PTMs), such as acetylation, lactylation, methylation, phosphorylation, ubiquitination, and glycosylation, play central roles in regulating diverse cellular processes, including signal transduction, metabolic adaptation, chromatin organization, and proteostasis. In cancer, PTM networks are extensively rewired, with profound alterations in enzyme levels, protein modification landscapes, and crosstalk among different modification types. These changes collectively shape key cancer hallmarks, such as sustained proliferative signaling, immune evasion, and therapeutic resistance. Recent advances in proteomic technologies have enabled comprehensive mapping of PTM landscapes and their regulatory mechanisms, facilitating the identification of PTM signatures associated with tumor subtyping, disease progression, and treatment response. This review summarized biomarkers and therapeutic targets associated with dysregulated PTM regulatory pathways in cancer.
Background Intervertebral disc degeneration (IVDD) is a major pathological process leading to low back pain, closely associated with the functional decline of nucleus pulposus progenitor cell (NPPC). The role of the cGAS-STING pathway in mediating DNA-sensing-associated inflammation and senescence in IVDD has not been fully elucidated.Methods This study integrated genetics, computational biology, cellular experiments, and animal models to systematically investigate whether taurine (TAU) exerts protective effects by modulating this pathway.Results Mendelian randomization analysis suggested a causal relationship between higher TAU levels and reduced risk of IVDD. Molecular docking and dynamics simulations demonstrated that TAU stably binds to cGAS and STING. In both degenerated human nucleus pulposus (NP) tissues and an H2O2-induced NPPC senescence model, the cGAS-STING pathway was significantly activated. TAU intervention maintained mitochondrial function, reduced cytosolic mtDNA leakage, and enhanced autophagic degradation of STING, thereby suppressing downstream TBK1-IRF3/NLRP3 inflammatory signaling and subsequently alleviating cellular senescence, inflammatory responses, and apoptosis. TAU treatment effectively delayed intervertebral disc height loss, histopathological progression, and pain sensitivity in a rat IVDD model.Conclusion This study is the first to reveal that TAU mitigates IVDD through multi-targeted modulation of the "mitochondria-cGAS-STING" axis, providing a theoretical foundation for its translational application as a disease-modifying agent.
Background Bladder cancer is the most common urological malignancy. Bladder cancer has limited therapeutic options, especially in advanced stages. Ferroptosis, an iron-dependent form of regulated cell death, has emerged as a promising target for cancer therapy. However, the role of autophagy in modulating ferroptosis remains incompletely understood.Methods We investigated the anti-tumor effects of JS-K, a nitric oxide-releasing prodrug, in bladder cancer through integrated cell, animal, and patient data studies. In vitro experiments with T24 and UM-UC-3 cells were used to explore how JS-K influences cancer cell survival and the interplay between autophagy and ferroptosis. In vivo, a BALB/c nude mouse tumor model provided a system to examine tumor response and tissue-level changes. To extend these findings to the clinical setting, we analyzed LC3B expression and its associations with ferroptosis-related genes, patient prognosis, and the tumor immune microenvironment.Results JS-K induced mitochondrial damage, lipid peroxidation, reactive oxygen species accumulation, and intracellular iron overload in bladder cancer cells in a concentration-dependent manner. These changes were accompanied by downregulation of GPX4 and SLC7A11 and upregulation of FTH1 and TFR1, indicative of ferroptosis. Inhibition or knockdown of the autophagy marker LC3B reversed these effects, establishing the role of autophagy in mediating ferroptosis. In xenograft models, JS-K suppressed tumor growth, an effect abrogated by LC3B silencing. Integrated transcriptomic and single-cell analyses revealed a strong correlation between LC3B and ferroptosis-related genes, with CISD1 identified as a key prognostic marker.Conclusions JS-K induces autophagy-dependent ferroptosis in bladder cancer cells and significantly suppresses tumor progression. Targeting the autophagy-ferroptosis axis offers a novel therapeutic strategy for bladder cancer treatment.
Circular RNAs (circRNAs) are a class of endogenous non-coding RNAs characterized by a covalently closed-loop structure. Although initially regarded as splicing byproducts, circRNAs are now recognized as essential regulators of gene and protein expression and play important roles in various human diseases. In recent years, growing evidence has indicated that a subset of circRNAs can be translated through cap-independent mechanisms to produce bioactive peptides or proteins. These findings expand the functional scope of circRNAs and offer new opportunities for RNA therapy. This review summarizes recent advances in circRNA biology, with an emphasis on their potential in diagnosis and treatment. We also review the therapeutic strategies targeting circRNAs at both the RNA and protein levels and the delivery systems that support circRNA-directed therapies. After we discuss how circRNA therapeutics may be integrated into precision medicine, we further highlight the current clinical progress and key challenges for advancing circRNA-based therapies toward clinical application.
Objective To investigate the inhibitory effect of the natural polyphenol Agrimol B on pancreatic ductal adenocarcinoma (PDAC) and its underlying molecular mechanisms.Methods The effects of Agrimol B on PDAC cell proliferation and apoptosis were assessed using Cell Counting Kit-8, colony formation, and flow cytometry assays. An in vivo PDAC xenograft mouse model was established for evaluation. Label-free quantitative proteomics, western blotting, immunofluorescence, and transmission electron microscopy were employed to analyze mitochondrial function, autophagy, and related signaling pathways. A patient-derived organoid model was used to evaluate the synergistic effects of Agrimol B with first-line chemotherapy drugs.Results Agrimol B significantly inhibited PDAC growth and induced apoptosis both in vitro and in vivo. Mechanistically, Agrimol B downregulated the expression of mitochondrial transcription termination factor 3, and promoted the accumulation of PTEN induced kinase 1 (PINK1) in mitochondria and Parkin translocation, thereby excessively activating PINK1/Parkin-dependent mitophagy. Concurrently, Agrimol B blocked lysosome biogenesis, leading to autophagosome accumulation and impaired autophagic flux. This dysfunctional autophagy ultimately mediated the anti-PDAC effect of Agrimol B. Furthermore, in PDAC patient-derived organoids, Agrimol B exhibited synergistic effects with first-line chemotherapy drugs such as gemcitabine and nab-paclitaxel.Conclusion Agrimol B exerts its anti-PDAC effects by downregulating mitochondrial transcription termination factor 3, hyperactivating PINK1/Parkin-mediated mitophagy, and obstructing autophagic flux. Its synergistic effect with chemotherapy drugs provides experimental evidence supporting its potential clinical translation.
Atherosclerosis is a disease centered on chronic inflammation, in which mitochondrial damage plays a key role in its initiation and progression. Traditionally, atherosclerosis is thought to be triggered by cholesterol accumulation, but recent studies have revealed that mitochondrial dysfunction has emerged as an important driving factor by inducing innate immune imbalance. In atherosclerosis, mitochondria undergo changes in membrane permeability, metabolic disorders, and dynamic imbalance due to oxidative stress and other factors, releasing mitochondrial damage-associated molecular patterns (mt-DAMPs). These mt-DAMPs activate innate immune pathways, promote the production of type I interferons and the release of pro-inflammatory factors such as interleukin 1β, and accelerate plaque progression. Mitophagy exerts a protective effect by eliminating damaged mitochondria. Specifically, the PINK1-Parkin pathway labels damaged mitochondria through ubiquitination; mitophagy receptors (such as NIX, FUNDC1, and BNIP3) directly bind to LC3 to initiate ubiquitination-independent mitophagy; and mitochondrial-derived vesicles selectively encapsulate damaged components and target them to lysosomes for degradation. All these processes can reduce mt-DAMP-induced damage and inhibit excessive immune activation. In this review, we summarize that innate immune imbalance caused by mitochondrial damage is a key mechanism for atherosclerosis progression. Mitochondrial quality control clears damaged mitochondria through multiple pathways, alleviates inflammatory responses and plaque burden, and provides potential targets for atherosclerosis treatment. Its precise regulatory mechanisms and drug development are future research directions.
Objectives:Gastric-type adenocarcinoma (GAS), an aggressive subtype of non-human papillomavirus (HPV)-associated (NHPVA) cervical adenocarcinomas (ADC), remains a treatment-refractory disease with poor prognosis. This study aims to explore the oncogenic mechanism and efficacious therapeutic target of GAS. Methods:We included 19 NHPVA and 153 HPVA ADC patients from our center to investigate clinicopathological features. We collected 3 GAS and 2 usual-type endocervical adenocarcinomas (UEA) for single-cell RNA sequencing and T-cell receptor sequencing. We conducted immunohistochemical staining of 25 GAS and 25 UEA samples and multicolor immunohistochemical staining of 2 GAS samples for validation. We explored the efficacy of anti-clusterin (OGX-011) and/or cisplatin (DDP) for GAS based on GAS-derived tumoroids. Results:Based on clinical data, we clinicopathologically verified the malignancy of GAS. Through single-cell RNA sequencing, we delineated key cell subtypes including GAS epithelial cells, "GAS-enriched fibroblasts", "GAS-associated γδT cells", and CD8+ exhausted T cells enduring heat stress and contributing to GAS aggressive phenotype. Regarding validation, we verified clusterin (CLU)-associated heat stress, highlighted the potential role of CLU-associated stress in promoting immune escape, and established a four-gene signature (CLU, PDGFB, TIGIT, and C3) indicating poor prognosis of GAS induced by CLU-associated stress and immune escape. Based on GAS-derived tumoroids retaining the histological features, CLU-associated stress, and genetic profile of parental tumor, we validated the anti-tumor and sensitizing DDP efficacy of targeting CLU. Conclusion:CLU-associated heat stress of key cell subtypes contributed to the malignant GAS microenvironment. Additionally, we pioneeringly constructed GAS-derived tumoroids and suggested that combining CLU-targeted treatment and DDP could improve the therapeutic efficacy for GAS.
Background Minor glomerular abnormalities (MGAs) are histopathologically heterogeneous renal lesions with subtle structural changes and latent clinical manifestations, yet their molecular mechanisms remain poorly characterized and underexplored. Methods In this study, we employed pressure cycling technology-assisted sample preparation combined with data-independent acquisition mass spectrometry to systematically compare the proteomic profiles of distant non-neoplastic tissues (n = 24) and MGA tissues (n = 27). Results A total of 9 529 protein groups were quantified with a false discovery rate < 1%, and 1 338 differentially expressed protein groups were identified (fold-change > 2 or < 0.5, P < 0.05), including 190 downregulated and 1 148 upregulated protein groups in MGA tissues. Gene ontology analysis revealed that the downregulated proteins were enriched in cell adhesion, ion binding, and molecular transport, whereas the upregulated proteins were enriched in transcriptional regulation, DNA replication/repair, and nucleic acid binding. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated inhibition of metabolic pathways and the peroxisome proliferator-activated receptor signaling pathway, as well as the activation of basal transcription factors and nucleotide excision repair in MGAs. Further screening revealed 13 core upregulated nuclear proteins (e.g. YY1, TAF9, RFC1, and POLR1D) with a >90% detection rate in MGA tissues; these proteins are functionally associated with renal inflammation, cell proliferation, and the DNA damage response. Conclusion Our study establishes a high-resolution proteomic landscape of MGAs, provides novel insights into their molecular pathogenesis, and identifies potential tissue biomarkers and therapeutic targets. The pressure cycling technology-assisted data-independent acquisition workflow also offers a robust technical framework for proteomic analysis of microscale renal biopsy samples.
Chimeric antigen receptor (CAR)-engineered immune cells have revolutionized cancer immunotherapy, expanding from the established success of CAR-T cells to a diverse array of cellular platforms. While seven Food and Drug Administration-approved CAR-T cell products demonstrate unprecedented efficacy in hematologic malignancies, significant limitations persist, including severe inflammatory toxicities, resistance in solid tumors, and manufacturing barriers. These challenges have catalyzed extensive research to extend CAR engineering into alternative effector cell types, such as unconventional T cell subsets, natural killer (NK) cells, macrophages, neutrophils, and dendritic cells, as well as non-immune platforms. Each cell type exhibits distinct antitumor mechanisms, persistence profiles, safety characteristics, and manufacturing requirements, positioning them to address complementary therapeutic needs. This review provides a comprehensive overview of diverse CAR-engineered cellular platforms, encompassing their biological properties, advantages, sourcing strategies, and manufacturing processes, alongside current clinical progress and optimization approaches. Beyond oncology, these platforms have demonstrated significant potential in treating autoimmune diseases, infections, cardiac fibrosis, and senescence-associated disorders. By leveraging distinct immune and non-immune cell types to mediate cytotoxicity or suppress pathogenic cells, CAR technology provides versatile therapeutic avenues across varied disease contexts. Through synthesis of recent advances in CAR platform diversity, this review identifies opportunities for targeted optimization and explores future directions for broadening CAR-based therapeutic applications.
The emergence of spatial genomics has introduced new possibilities to studying structure-function relationships in neuropsychiatric disorders. Spatial transcriptomics (ST) allows the detection of thousands of genes simultaneously up to single-cell resolution which holds spatial location of gene transcriptional activity within a tissue sample. Spatial genomics technologies are developed rapidly, and many of them were used for constructing brain spatial genomics atlases. A brain spatial transcriptomic atlas is a map of the gene expression across brain regions in situ—that is, within their anatomical context—often at single-cell or near-single-cell resolution. The brain spatial genomics atlas has been constructed for a few species including mice and humans. These brain atlases can be used to further investigate specific genes or pathways that are dysregulated in disease, advancing therapeutic development as a result. The spatial genomics and brain ST atlas are vital for driving precision medicine efforts for neurological disorders.
