Alternative splicing (AS) significantly enhances transcriptomic diversity, and its dysregulation is implicated in numerous human diseases. However, no public database systematically compiles sex-related AS events across human tissues. We developed SASdb (http://www.gdbioinfo.top/sasdb), a comprehensive database contains 2,951,059 AS events and 46,418 sex-biased alternative splicing (SAS) events, covering 22 human tissues. SASdb reveals extensive sex-specific splicing patterns, offering new insights into molecular sex differences. A case study on NSCLC-specific SAS events, absent in healthy tissues, highlights their enrichment in cancer-related pathways like autophagy, GPI-anchor biosynthesis, and AMPK/mTOR signaling. SASdb’s intuitive visualization supports research in sex biology and precision medicine.

OSW-1, a steroidal disaccharide isolated from the bulbs of Ornithogalum saundersiae, has been extensively studied for its extremely potent cytotoxicity against the National Cancer Institute's 60 cancer cell lines with an average IC50 of 0.78 nM, while exhibiting selectivity toward normal cells. Although OSBP and ORP4L have been identified as its binding targets, their known functions appear insufficient to account for the compound's exceptional potency, suggesting the involvement of additional mechanisms and targets. Therefore, elucidating novel target proteins associated with its activity is essential for the further development of this molecule. Here, we disclose that OSW-1 can block the glycolytic pathway and trigger compensatory mitochondrial oxidative phosphorylation. This previously uncharacterized mechanism is relevant to the key rate-limiting enzyme, enolase 1 (ENO1), which shows subnanomolar affinity with OSW-1. Our study repurposes OSW-1 to be a small-molecule probe to investigate the function of ENO1 and a promising candidate for metabolism-targeted anticancer therapy.

Double-Negative T (DNT) cells, lacking both CD4 and CD8 expression, play critical roles in cancer immunology, and have garnered increasing attention in cancer research. However, their heterogeneity and functional diversity within the tumor microenvironment (TME) remain underexplored. In-house and publicly available single-cell RNA sequencing (scRNA-seq) data for different cancer types were integrated after quality control and batch effect correction, followed by DNT cells separation from CD3+ T cells subtypes. Functional characteristics, intercellular communication, differentiation trajectories, regulatory networks, and clinical relevance were analyzed among different DNT subsets. Key findings were validated using multiplex immunofluorescence and spatial transcriptomics to investigate the spatial localization of DNT subsets and their interactions within the TME. Impact of γδ T cells on immunotherapy response was also assessed using MC38-based murine tumor model. By integrating scRNA-seq data from 2,369 samples across 23 cancer types, we established a comprehensive single-cell atlas of 157,025 high-quality DNT cells. Fourteen distinct DNT subsets (6 αβ DNT and 8 γδ T cell subsets) were identified, demonstrating tumor both type-specific and shared distribution patterns, as well as unique cell-cell interaction network within the TME. These subsets displayed specialized functional profiles, including cytotoxicity, antigen presentation, and immune modulation, indicating that the functional diversity of DNT cells is largely subset-specific rather than a manifestation of multifunctionality within a single population. We also delineated divergent trajectories for αβ DNT and γδ T cell subsets, including the functional plasticity of gut-resident γδ T cells transitioning between cytotoxic and immunosuppressive states. Notably, several DNT subsets were significantly associated with favorable clinical treatment outcomes, including improved responses to cancer immunotherapy. Consistently, depletion of γδ T cells in the murine tumor model significantly decreased the efficacy of PD-1 blockade, underscoring their critical role in therapeutic response. Our study uncovers the previously underappreciated heterogeneity and functional diversity of DNT cells in the TME and demonstrates their profound impact on tumor progression and immunotherapy outcomes.

Despite remarkable advances in cancer therapy, clinical outcomes remain limited by drug resistance, metastasis, and off-target effects that stem from the complexity and heterogeneity of tumors. The "hallmarks of cancer" provides a systematic framework for understanding tumor biology and identifying therapeutic targets. However, the expression patterns and mechanistic dependencies of these hallmarks differ markedly among cancer types. Autophagy is an evolutionarily conserved catabolic process, exerting multifaceted and context-dependent functions in tumor initiation and malignant progression. In this review, we summarize current insights into the regulation of autophagy and its impact on key signaling pathways. Most importantly, based on the characteristics of tumor progression, we classified the 14 hallmarks of cancer into four categories and discussed the crosstalk between autophagy and these hallmarks. In addition, we survey recent progress in the discovery of small-molecule compounds targeting autophagy and evaluate their therapeutic implications from a hallmark-oriented perspective. Finally, this review highlight that integrating the conceptual framework of cancer hallmarks with the biological and pharmacological functions of autophagy offers a promising avenue for precision oncology. Elucidating how autophagy differentially modulates distinct hallmarks, as synthesized in this review, will be instrumental in facilitating context-specific interventions and guiding future strategies for personalized cancer therapy.

Aging is linked to a higher incidence of gut diseases such as inflammatory bowel disease (IBD), yet the underlying mechanisms remain unclear. We identified an age-related decline in magnesium (Mg) levels specifically in the gut across species, prompting investigation of its role in intestinal health. Functional studies demonstrated that Mg restriction accelerates gut aging in old but not in young mice and aggravates colitis severity. Multi-omics analysis of mouse tissues revealed that dietary Mg deficiency reshapes the phosphoproteome and N-glycoproteome, destabilizing adhesion complexes, a hallmark of intestinal aging and inflammation. In the UK Biobank cohort (n = 182,213), dietary Mg intake was inversely correlated with gut disorder risk, with 334.7-420.0 mg/day conferring significant protection against Crohn's disease, ulcerative colitis, irritable bowel syndrome, and diverticular disease. These findings identify Mg homeostasis as a key regulator of gut health and highlight Mg supplementation as a potential strategy to counteract age-related gut dysfunction.

Advancements in cancer biology have increasingly highlighted the crucial role of sex in influencing cancer progression and therapeutic outcomes. Nevertheless, current research remains largely focused on overall populations, overlooking the impact of sex. This gap underscores the need for a detailed understanding of how sex differences manifest within the tumor microenvironment (TME). We performed a comprehensive analysis of sex differences by integrating a large-scale single-cell RNA sequencing atlas comprising 1,662 samples from fourteen human cancer types. Systematic profiling of the TME was conducted to identify sex-specific differences, including SPP1+ macrophages. Furthermore, we compared anti-PD-1 immunotherapy responses between male and female mice, including a macrophage-specific Spp1 knockout model. Our analysis revealed pronounced sex-specific differences in key TME components, with females showing significantly higher proportions of myofibroblastic cancer-associated fibroblasts, SPP1+ macrophages, and exhausted CD4+ T cells than males. Experimentally, anti-PD-1 therapy was more effective in males than females in mice, and macrophage-specific Spp1 knockout could sensitize female mice to anti-PD1 immunotherapy. This study reveals that sex shapes TME composition and drives divergent therapeutic responses, establishing sex as a critical variable in personalized cancer care and supporting sex-informed strategies to improve immunotherapeutic outcomes.

Subsequently to the publication of the above paper, an interested reader drew to the authors' attention that, concerning the Transwell migration assay experiments shown in Fig. 6F on p. 1940, the 'NC' and 'siTEAD3' experiments showed an overlapping section of data, such that data which were intended to show the results from differently performed experiments had apparently been derived from the same original source. The authors proposed removing Fig. 6F from the figure, as they considered that the conclusions of these experiments were sufficiently well supported by the data shown in Fig. 6D and E, although the Editor expressed to them our preference that the authors should repeat these experiments, if necessary, to rectify the original errors made during the inaccurate assembly of data in Fig. 6F. The authors were willing to perform the requested experiments, and the revised version of Fig. 6, showing the replacement data for the migration assay experiments in Fig. 6F, is shown on the next page. The authors wish to draw the readers' attention to the fact that the statistical significance of the experiments featured in the new Fig. 6F was not exactly the same as that in the original figure (note the change to the wording of the figure legend opposite, which is highlighted in bold); however, the conclusion that knocking out TEAD family proteins significantly inhibits the migration of MDA-MB-231 cells is completely consistent with the conclusion of the original article. This difference in the statistical significance of the results is reflected in a proposed change of the wording to describe the results of Fig. 6F in the manuscript; therefore, the final sentence of the Results section, left-hand column on p. 1941, should now read as follows: 'As shown in the results of the cell migration assay (Fig. 6F), knockdown of TEAD family proteins inhibits the migration of MDA-MB-231 cells'. The authors regret the errors that were made during the preparation of the Fig. 6. They are grateful to the editor of Oncology Reports for allowing them the opportunity to publish this Corrigendum, and all the authors agree to this publication. Furthermore, they apologize to the readership for any inconvenience caused. [Oncology Reports 43: 1928-1944, 2020; DOI: 10.3892/or.2020.7563].

Post-translationally modified proteins are crucial autoantigens in autoimmune diseases, with citrullinated proteins being key targets of autoantibodies in rheumatoid arthritis (RA). However, accurate citrullinome profiling and autoantigen identification remain limited by insufficient detection methods and computational tools. Here we develop Iseq-Cit (internal standard-assisted enrichment-free approach for high-throughput quantitative analysis of citrullinome), for global citrullinome profiling in individuals at RA risk and in patients with RA across a longitudinal cohort, requiring less than 1% of the sample input needed for conventional methods. We find that plasma citrullinome profiles closely correlate with RA development and severity. Moreover, we develop models integrating clinical indicators and citrullination data, achieving high accuracy in predicting treatment response. To evaluate the RA-sera reactivity of identified citrullinated peptides, we train a bidirectional gated recurrent unit model using 67,399 RA-sera negative and 8,816 RA-sera positive peptides. External validation through enzyme-linked immunosorbent assays confirms 84.2% accuracy in predicting RA-sera reactivity of citrullinated peptides, yielding 19 promising candidates for RA diagnosis. This work provides strategies for citrullinated peptide identification, autoantigen discovery and RA treatment stratification.

Importance:Locally advanced, unresectable esophageal squamous cell carcinoma (ESCC) has a poor prognosis despite definitive chemoradiotherapy (CRT), and no standard maintenance therapy currently exists. Personalized vaccines targeting tumor neoantigens combined with immune checkpoint inhibitors may enhance antitumor immunity, potentially improving these patients' outcomes. Objective:To evaluate whether maintenance therapy with a personalized neoantigen dendritic cell vaccine (Neo-DCVac) combined with camrelizumab improves overall survival (OS) compared to camrelizumab alone in patients with unresectable locally advanced ESCC following definitive CRT. Design setting and participants:The CHANT-241 trial is a randomized, open-label, single-center, phase 2 clinical trial enrolling 165 patients aged 18 to 80 years with histologically confirmed unresectable locally advanced ESCC. Eligible participants must have completed definitive chemoradiotherapy (CRT) and undergone radiologic assessment within 3 to 5 weeks demonstrating no evidence of disease progression. Prior immunotherapy is allowed. Additional inclusion criteria include the ability to provide fresh tumor tissue or archived pathology slides of sufficient quality. Patients are randomized in a 2:1 ratio to receive either combination therapy or camrelizumab alone. Intervention:Patients in the experimental group receive Neo-DCVac (0.5-2 × 107 cells per dose, subcutaneously, following cyclophosphamide pretreatment), administered as 5 priming doses and 10 booster doses over a 12-month vaccination period, in combination with camrelizumab (200 mg intravenously every 4 weeks). Patients in the control arm receive camrelizumab alone at the same dose and schedule. Main outcomes and measures:The primary endpoint is the 2-year OS rate. Secondary endpoints include OS, progression-free survival (PFS), treatment-related adverse events (TRAEs), and exploratory biomarker analyses, including tumor mutational burden (TMB), PD-L1 expression, and circulating tumor DNA (ctDNA). Results:Clinical outcomes are not yet available. Upon completion of enrollment and data analysis, the study findings will be disseminated through publication in a peer-reviewed journal. Conclusions:The CHANT-241 trial is designed to evaluate whether the addition of Neo-DCVac to camrelizumab as maintenance therapy improves survival outcomes in patients with unresectable locally advanced ESCC. The findings aim to provide high-level evidence supporting a novel precision immunotherapy approach in this population. Clinical Trial Registration:ClinicalTrials.gov, identifier NCT06675201.

Pediatric sepsis is a systemic inflammatory syndrome caused by dysregulated host immune responses, with a high mortality rate and a lack of effective biomarkers, posing significant challenges for early diagnosis and treatment. This study integrated six bulk RNA-seq datasets related to pediatric sepsis, including 497 patients and 116 healthy control samples. Weighted gene co-expression network analysis was used to identify gene modules significantly associated with pediatric sepsis, and 237 high-confidence biomarkers were screened based on 14 machine learning models, among which RORA and GPR183 stood out in multiple models. Functional analysis indicated that these biomarkers were mainly involved in biological processes such as transcription and translation, the immune system, and cellular senescence. Immune infiltration analysis revealed a significant reduction in adaptive immune cells such as B cells and CD8+ T cells and an increase in neutrophil and monocyte infiltration in pediatric sepsis patients, consistent with the “immunoparalysis” theory. Notably, RORA and GPR183 were positively correlated with CD8+ T cells, suggesting their potential role in regulating T cell function. Additionally, we developed an open-source website for real-time application of biomarkers. Furthermore, we established a sepsis model in zebrafish and found that rora1, rora2, and gpr183 expression levels were significantly downregulated in the disease group. This study provides new insights for developing novel diagnostic tools and targeted therapies for pediatric sepsis.

​Background: Tumor transcriptomes reflect not only malignant cells but also diverse stromal and immune populations within the tumor microenvironment. Although bulk RNA sequencing has identified numerous prognostic gene signatures across cancers, the cellular origins of these signals remain poorly resolved. Methods: We integrated bulk transcriptomic and clinical data from 16 The Cancer Genome Atlas (TCGA) cancer types with pan-cancer single-cell RNA sequencing datasets from 10 tumor types to construct a cell-type-resolved atlas of prognostic genes. Prognosis-related differentially expressed genes (DEGs) were identified by combining tumor-versus-normal differential expression analysis with survival analysis. Their cellular origins were annotated using the Human Protein Atlas (HPA) and pan-cancer single-cell transcriptomic data. Gastric cancer was used for protein-level validation by immunohistochemistry (IHC) on a tissue microarray cohort. Findings: Across 16 cancer types, we identified 14,896 prognosis-related DEGs, including 8,303 protein-coding genes. Most prognostic genes were cancer-specific, whereas only a small subset was shared across multiple tumor types, indicating substantial context dependency of prognostic transcriptional programs. Integration with HPA and single-cell datasets enabled annotation of the majority of prognostic genes to specific cellular compartments. At single-cell resolution, stromal cells accounted for the largest fraction of cell-type-specific prognostic genes. Notably, among poor-prognosis genes with clear cellular annotation, stromal-derived genes represented the predominant category, whereas lymphoid-cell contributions were relatively limited. In gastric cancer, microfibrillar-associated protein 4 (MFAP4) was identified as a stromal-associated prognostic candidate and further validated by IHC, which showed predominant stromal expression and an independent association with poorer overall survival in multivariable analysis. Interpretation: This study establishes a pan-cancer, cell-type-resolved atlas of prognostic genes and provides a framework for interpreting bulk prognostic transcriptomic signals in their cellular context. These findings show that adverse prognostic signals are shaped predominantly by non-malignant cellular programs, particularly stromal compartments, and support the development of cell-context-aware prognostic biomarkers.

Background Pregnancy complications frequently co-occur, yet existing risk assessment tools primarily count comorbidities without weighting their relative severity or accounting for socioeconomic determinants of health. We aimed to develop and internally validate a simplified cumulative complication burden score (sCCBS) for predicting preterm birth at the time of hospital admission for delivery. Methods We conducted a retrospective cohort study of 43,773 vaginal deliveries at a tertiary hospital in eastern China (2014–2024). This is an admission-based risk assessment tool, not a prenatal screening instrument. Candidate predictors included 15 pregnancy complications present at admission and two socioeconomic proxies (advanced maternal age > = 35 years, non-local residence). Variable selection employed LASSO regularization with 5-fold cross-validation, followed by exact logistic regression for weighting. Weights were scaled to integers to create the sCCBS. Internal validation used bootstrap resampling (1000 iterations). Temporal validation was performed using a chronological split (2014–2020 training, 2021–2024 validation). Model performance was assessed using the AUC, calibration plots, and decision curve analysis. The optimal cutoff was determined by the Youden index. The study was reported per TRIPOD guidelines. Results The final sCCBS comprised four weighted components: PROM at admission (+ 7 points), gestational diabetes mellitus (+ 2), advanced maternal age (+ 2), and non-local residence (+ 1). The sCCBS showed moderate discriminative ability for preterm birth prediction (AUC = 0.717, 95% CI: 0.705–0.729), comparable with established obstetric prediction models. Temporal validation demonstrated excellent stability (training AUC = 0.708, validation AUC = 0.734, Delta = 0.026). The optimal cutoff (Youden = 0.387) yielded sensitivity 60.8%, specificity 78.8%, PPV 10.7%, and NPV 97.9%. Risk stratification identified three clinically meaningful groups: low risk (0–1 points, PTB rate 1.9%), moderate risk (2–3 points, 3.0%), and high risk ( > = 4 points, 10.6%). The sCCBS significantly outperformed simple complication counting (Delta AUC = + 0.080, P < 0.001) and the simplified OB-CMI (Delta AUC = + 0.021, P = 0.002). Decision curve analysis confirmed positive net benefit across clinically relevant risk thresholds (1%-16%). Conclusions The sCCBS is a simple, interpretable admission-based tool for obstetric risk stratification that incorporates both medical complication burden and socioeconomic determinants. By quantifying the cumulative impact of pregnancy complications present at hospital admission, the score addresses a gap in current intrapartum risk assessment and may facilitate early identification of high-risk pregnancies upon admission for delivery. External validation is warranted to confirm generalizability.

ABSTRACT Early‐onset colorectal cancer (EOCRC) is increasing worldwide, yet the molecular basis underlying its age‐related heterogeneity remains insufficiently defined. To address this gap, we performed whole‐exome sequencing in a Chinese EOCRC cohort diagnosed before 40 years of age ( n = 111), bulk transcriptome sequencing in a subset of these tumors ( n = 59), and whole‐exome sequencing in an independent Chinese colorectal cancer cohort spanning a broader age range ( n = 210). We then integrated these data with publicly available somatic mutation, bulk RNA‐seq, and single‐cell transcriptomic datasets to characterize age‐associated tumor‐intrinsic and microenvironmental features. Genomic analyses revealed a distinct EOCRC landscape, including lower frequencies of APC and KRAS mutations, more frequent SMAD4 disruption through mutation or copy‐number loss, and enrichment of the PTPRK‐RSPO3 fusion. Single‐cell analyses further showed increased infiltration of CD4 + memory T cells and mast cells in EOCRC, whereas later‐onset colorectal cancer was characterized by SPP1 + macrophage predominance and a strengthened interaction axis between FAP + cancer‐associated fibroblasts and SPP1 + macrophages. Therapeutic evaluation in aged mouse models, together with single‐cell analysis of immunotherapy‐treated patients, indicated reduced PD‐1 blockade efficacy with increasing age. Together, these findings support age‐informed molecular classification and therapeutic stratification in colorectal cancer.

Fibrosis is a severe pathological outcome of many chronic diseases, yet the therapeutic potential of targeting the altered major histocompatibility complex (MHC) class I immunopeptidome remains largely unexplored. Here we characterized the MHC class I immunopeptidomes from both fibrotic foci of human idiopathic pulmonary fibrosis lung explants and bleomycin-treated mice, identifying a diverse repertoire of fibrosis-associated peptides. Parallel profiling of bleomycin-induced pulmonary fibrosis in mice enabled the computational prioritization of therapeutic targets. In vivo, therapeutic vaccination with three candidate peptides (MAF116-124, APBB270-78 and TNS3119-127) effectively mitigated fibrosis progression in bleomycin-treated mice. Furthermore, leveraging its evolutionary conservation, we found that MAF116-124 elicited specific human cytotoxic T lymphocytes that lysed human idiopathic pulmonary fibrosis-derived myofibroblasts and M2-like macrophages. This study indicates that immunopeptidome profiling provides a robust platform for discovering translatable antifibrotic immunotherapies.

Use of immune checkpoint inhibitors (ICIs) has significantly improved patients' survival, especially in lung cancer. However, immunotherapy-related adverse events (irAEs) frequently occur and negatively impact patients' quality of life. While investigations into genetic predictors of irAEs remain ongoing, no robust genetic loci predictive of these toxicities have been definitively established to date. To investigate the pharmacogenomic markers related to irAEs of PD-1/PD-L1 inhibitors in lung cancer patients, we collected blood specimens from 1467 patients. After rigorous screening and quality control procedures, 785 of these patients were enrolled in a two-stage genome-wide association study (GWAS). The study comprised an initial discovery phase, in which 455 patients underwent microarray-based analysis, and a subsequent validation phase with an independent cohort of 330 patients. Of 688,783 SNPs genotyped using whole genome-wide microarray screening, 52 SNPs were validated using MassARRAY system. The potential impact of significant variants investigated by eQTL analysis. We identified three novel SNPs that are significantly associated with irAEs of PD-1/PD-L1 inhibitor treatments in these lung cancer patients in both discovery and validation cohorts, rs192921786 (discovery: P = 4.09 × 10-7, OR = 9.57; validation: P = 0.043, OR = 4.42) for pneumonitis, rs2498632 (discovery: P = 1.85 × 10-6, OR = 0.50; validation: P = 0.021, OR = 0.65) for anemia and rs17080141 (discovery: P = 9.11 × 10-7, OR = 3.16; validation: P = 0.027, OR = 1.86) for thrombocytopenia. Lung cancer patients with rs192921786 T allele, rs2498632 C allele, and rs17080141 A allele were more likely to suffer immunotherapy related pneumonitis, anemia and thrombocytopenia, respectively. In conclusion, rs192921786, rs2498632 and rs17080141 are novel candidate risk loci for pneumonitis, anemia, and thrombocytopenia in lung cancer patients receiving immunotherapy. These findings warrant further investigation and validation to assess their potential as predictive biomarkers.