Ningbo Medical Center Lihuili Hospital

Understanding biological processes requires spatiotemporal mapping of proliferative and transcriptional dynamics. Current spatial transcriptomics methods capture only protein-coding transcripts and static snapshots, obscuring non-coding RNAs (ncRNAs) and dynamic events. We developed SPTEdU-seq, integrating spatial total transcriptomics with 5-ethynyl-2'-deoxyuridine tracking to co-profile gene expression and proliferation dynamics. SPTEdU-seq demonstrates ultrahigh sensitivity for coding and non-coding transcripts and for splicing isoforms, with single-molecule probe design eliminating optical imaging. Applied to developing and adult mouse brains, it revealed spatial lncRNA patterns, reconstructed developmental trajectories, and enabled spatiotemporal lineage tracing. In murine ischemic stroke, it mapped regeneration dynamics and identified an Igfbp5+ astrocyte subtype within a pro-repair niche. In mouse and human renal tumors, it uncovered tumor-associated splicing and detected diagnostic 3p loss. By profiling newborn and resident cells in intact microenvironments, it unveiled previously inaccessible interaction networks. SPTEdU-seq thus establishes a powerful framework for investigating cell fate dynamics in regeneration, development, and cancer.

The online version contains supplementary material available at 10.1007/s13205-026-04756-5.

Lung adenocarcinoma (LUAD) is a major subtype of lung cancer that frequently develops brain metastases. Tumor heterogeneity substantially complicates disease management, and reliable biomarkers for metastatic progression remain lacking. LIM domain kinase 1 (LIMK1), a key regulator of cytoskeletal dynamics, has been implicated in tumor progression; however, its role in regulating brain metastasis in LUAD remains unclear. Single-cell RNA sequencing data from 11 primary LUAD tumors and 10 brain metastases were analyzed to identify malignant epithelial subclusters associated with metastatic dissemination. Tumor evolutionary trajectories and gene regulatory networks were explored using pseudotime trajectory analysis and weighted gene co-expression network analysis. LIMK1 expression was validated using The Cancer Genome Atlas dataset, as well as RT–qPCR and Western blotting in LUAD tissues and cell lines. Functional assays, including cell proliferation, colony formation, migration, and invasion, were performed following LIMK1 knockdown in LUAD cell lines. Six malignant epithelial subclusters were identified, among which clusters 0 and 4 were significantly enriched in brain metastases and associated with poor survival outcomes. LIMK1 was identified as a hub gene within these metastasis-associated clusters. LIMK1 expression was markedly upregulated in LUAD tissues and cell lines, and elevated LIMK1 levels predicted an unfavorable prognosis. Functional experiments demonstrated that LIMK1 depletion significantly inhibited tumor cell proliferation, migration, and invasion, while partially reversing epithelial–mesenchymal transition (EMT). Mechanistically, LIMK1 was found to promote LUAD progression through activation of the PI3K/AKT/mTOR signaling pathway. LIMK1 represents a novel prognostic biomarker and metastasis-associated regulator in LUAD. By driving EMT and activating PI3K/AKT/mTOR signaling, LIMK1 facilitates malignant progression, highlighting its potential as a therapeutic target for LUAD patients with brain metastases.

Esophageal cancer is a malignancy to cause heavy global disease burden, the research of traditional risk factors, such as smoking, alcohol use, can not fully explain the heterogeneity of region specific incidence and molecular diversity of esophageal cancer. Traditional risk factor research usually focus on isolated effects of individual factor, neglecting interaction of multi factors on subtypes of esophageal cancer, and the exposure assessment of traditional risk factor research can not quantify the actual biological doses of potential risk factors, such as micronutrient deficiency and region-specific environmental pollutant exposure. Advancements in multi-omics technologies (including exposomics and genomics) have identified emerging risk factors, which have not been formally classified as established risk factors for esophageal cancer by International Agency for Research on Cancer, but revealed the non-traditional risk factors (potential carcinogenic mechanisms or population-level associations) of esophageal cancer in the past decade, including oral microorganism dysbiosis, perfluoroalkyl and polyfluoroalkyl substance exposures, and circadian disruption. This paper systematically summarizes the progress in epidemiological research of these factors to provide novel perspectives for the precise prevention and control of esophageal cancer.

To compare the predictability of central corneal thickness (CCT) reduction in myopic patients undergoing femtosecond laser-assisted in situ keratomileusis (FS-LASIK) using the aberration-optimized (Triple-A) and topography-guided (TG) profiles on the MEL 90 platform. This study involved 82 patients, treating one eye with the Triple-A profile and the other with the TG profile on the MEL 90, with an average spherical equivalent of - 5.76 ± 2.02 D (Triple-A) and - 5.79 ± 1.90 D (TG). Refractive assessments were done preoperatively and at 1day, 1week, 1month, and 3months postoperatively. Achieved CCT reduction (via Pentacam) = CCTpre-op-CCTpost-op. The MEL 90 platform provided the predicted CCT reduction, and comparative statistical methods and linear regression analyses were conducted. The 3-month CCT reduction was underestimated by 5.18 ± 7.41μm in the Triple-A group (P < 0.0001) and by 14.44 ± 10.10μm in the TG group (P < 0.0001). The planned CCT reduction in the TG group was much smaller than that in the Triple-A group (P < 0.0001), yet the achieved reduction was greater (P = 0.034), mainly in moderate myopia (P = 0.012). Moreover, subgroup analyses indicated that these differences were present exclusively in moderate to high myopia. As the corrected refraction increased, the planned-achieved difference (PAD) also increased. For patients with moderate and high myopia, both Triple-A and TG profiles of FS-LASIK on the MEL 90 laser platform may underestimate the CCT reduction. TG LASIK does not save corneal tissue but even consumes more of it in moderate myopia.

Breast cancer remains a leading global health concern in women, while screening is still limited by imaging accessibility and reduced sensitivity in dense breasts. Here we conduct a multicenter case-control study including 503 breast cancer patients and 289 benign controls to develop TuFEst, a machine learning model based on genome-wide cell-free DNA fragmentomic features. TuFEst achieves high sensitivity (95%) and specificity (78.3%) for early cancer detection and reliably identifies malignancies missed by conventional imaging. Extension of this framework enables non-invasive molecular subtyping (TuFEst-MS) and lymph node status prediction (TuFEst-LN), with strong performance in independent validation cohorts and imaging-pathology discordant cases. Transcriptomic profiling of paired bulk tumor samples (n = 79) demonstrates that elevated TuFEst-derived cancer scores reflect tumor aggressiveness and immune-related biological programs. Together, these findings support cfDNA fragmentomics as an integrated liquid biopsy strategy for breast cancer management, enabling concurrent detection, molecular subtyping, and lymph node evaluation with potential clinical utility.

Intestinal aging characterized by imbalance between cell senescence and mucosal self-renewal, increases susceptibility to the elderly-onset ulcerative colitis (UC), while the underlying mechanisms remain elusive. Here, we identify mRNA N4-acetylcytidine (ac4C) modification and its specific writer, N-acetyltransferase 10 (NAT10), as critical regulators of human colonic epithelial cell senescence. Knockdown of NAT10 significantly alleviates human colonic epithelial cell senescence in vitro and colonoid and intestinal aging in vivo in aged mice. Using ac4C-modified transcriptome sequencing, we reveal that NAT10 stabilizes DYRK1A mRNA through ac4C modification, thereby driving colon epithelial senescence. Moreover, NAT10 and DYRK1A are markedly upregulated in ulcerative colitis tissues from elderly patients and positively correlate with disease severity. Knockdown of NAT10, treatment with Nat10 or Dyrk1a inhibitor, alleviates colitis in aged mice. Collectively, these findings suggest that modulating NAT10-mediated RNA ac4C modification could rejuvenate intestinal aging and provide a novel therapeutic strategy for elderly-onset colitis.

BackgroundCirrhosis, particularly HBV-induced, poses a significant global health burden. This study compares immune cell landscapes in HBV and non-viral cirrhosis using single-cell RNA sequencing (scRNA-seq) to elucidate distinct immune mechanisms driving disease progression.MethodsLiver tissues from HBV cirrhosis patients and healthy controls were analyzed via scRNA-seq. Public single-cell and spatial transcriptomics data were integrated to map immune cell populations. Computational analyses included differential expression, pathway enrichment (KEGG/GO), and cell–cell communication (CellChat).ResultsHBV cirrhosis exhibited expanded Macrophage-PLCG2 (anti-inflammatory) and CD8 + T-FABP5 subsets, while Macrophage-CD5L, CD4 + T-ANXA1, CD4 + T-CCR6, and NK-FCER1G were reduced. Pathway analysis linked Macrophage-PLCG2 to Rap1 signaling, whereas Macrophage-CD5L associated with lysosomal pathways. Spatial analysis revealed myeloid-T cell colocalization in HBV cirrhosis. Enhanced HLA-E/KLRK1 signaling between myeloid and NK cells was identified in HBV cases (p < 0.05).ConclusionThis study delineates immune cell heterogeneity between HBV and non-viral cirrhosis, highlighting potential therapeutic targets like Macrophage-PLCG2 and CD8 + T-FABP5. Findings underscore the role of immune dysregulation in HBV cirrhosis progression.