Immunotherapy resistance presents a formidable challenge in tumor biology. While fibroblast growth factor receptor 3 (FGFR3) serves as a pivotal oncogenic driver in a multitude of cancers, the exploration of its role in immune checkpoint inhibitor (ICI) resistance remains scarce, thus impeding a deeper understanding of the tumor immune microenvironment (TIME) in the era of immunotherapy. Employing patient-derived urothelial carcinoma (UC) organoids and co-cultured systems, along with single-cell RNA sequencing (scRNA-seq), whole-exome sequencing (WES), bulk RNA-seq, and CUT& Tag epigenomics in UC cohorts, we identified and characterized the key downstream mediators of FGFR3. The TIME associated with FGFR3 mutations exhibited a depletion of NK and CD8+ T cells, while simultaneously harboring an accumulation of exhausted effectors, correlating with diminished ICI response. Erdafitinib reprogrammed this "cold" TME into an inflamed state through a novel FGFR3-STAT5-IRF2 signaling cascade. These findings, corroborated by a wealth of evidence, advocate for the combination of FGFR3-targeted therapy with immunotherapy for UC, bridging critical pre-clinical and clinical insights.

RATIONALE:N6-methyladenosine (m6A) modifications are implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD), yet the precise role of the demethylase fat mass and obesity-associated protein (FTO) remains unclear. OBJECTIVES:To identify whether FTO acts as a suppressor of COPD pathogenesis and to elucidate the underlying epitranscriptomic mechanism. METHODS:COPD models were established using cigarette smoke-exposed mice and cigarette smoke extract-stimulated BEAS-2B cells. FTO expression was modulated by lentiviral transduction. m6A epitranscriptomic microarray, RNA immunoprecipitation, m6A methylation analysis, and mRNA stability assays were performed. Inflammation, oxidative stress, mitophagy, and ERK1/2-Drp1 signaling were assessed. RESULTS:FTO expression is reduced in COPD patients and murine models, correlating with elevated m6A levels and disease severity. Overexpression of FTO mitigates inflammation, oxidative stress, and mitochondrial dysfunction by destabilizing S100 calcium-binding protein A9 (S100A9) mRNA via m6A demethylation. Mechanistically, FTO inhibits the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2)- dynamin-related protein 1 (Drp1), thereby suppressing excessive mitophagy and preserving mitochondrial integrity. Notably, S100A9 overexpression abolishes the protective effects of FTO, establishing the FTO/S100A9 axis as a central regulator. CONCLUSIONS:FTO attenuates COPD pathogenesis by demethylating S100A9 mRNA, thereby suppressing ERK1/2-Drp1-driven mitophagy. The FTO/S100A9 axis represents a novel epitranscriptomic mechanism and a potential therapeutic target for COPD.

OBJECTIVE:To develop a transcriptomic-based recurrence prediction model for non-muscle-invasive bladder cancer (NMIBC), to comprehensively validate its efficacy in an independent Chinese cohort, and to explore the underlying biological mechanisms driving tumor recurrence. METHODS:Transcriptome profiling data from the multicenter European Urothelial Cancer Molecular Classification Consortium (UROMOL) cohort (n=535) were used as the training cohort. The least absolute shrinkage and selection operator (LASSO) Cox regression was employed to identify prognostic genes and construct a risk score model. Internal validation was strictly performed using Bootstrap resampling and 10-fold cross-validation. External validation was conducted in an independent Chinese cohort (n=85) from Peking University People ' s Hospital. Gene set enrichment analysis (GSEA) was applied to elucidate the distinct biological differences between high- and low-risk groups. RESULTS:A 36-gene prognostic signature was identified from 12 170 genes to construct the risk score model. In the training cohort, the model achieved a concordance index (C-index) of 0.702 (95%CI: 0.664-0.740), with 1-, 3-, and 5-year areas under the receiver operating characteristic curve (AUC) of 0.782, 0.811, and 0.799, respectively. The 5-year recurrence-free survival (RFS) rates for the high- and low-risk groups were 35.2% and 72.8%, respectively (Log-rank P < 0.001). Internal validation via Bootstrap (C-index=0.702) and 10-fold cross-validation (C-index=0.708) demonstrated robust stability. In the independent Chinese validation cohort, the model maintained a favorable C-index of 0.685 (95%CI: 0.631-0.739), with 1-, 3-, and 5-year AUC of 0.705, 0.743, and 0.665, respectively. Its predictive performance was comparable to the traditional European Organization for Research and Treatment of Cancer (EORTC) risk score (C-index=0.652). GSEA revealed that the low-risk group was enriched in energy metabolism and protein homeostasis pathways, while the high-risk group was associated with extracellular matrix (ECM) remodeling and cell adhesion pathways. CONCLUSION:The 36-gene signature developed in this study demonstrates favorable predictive performance and stability across both the training and independent Chinese cohorts. While exhibiting comparable predictive efficacy to the traditional EORTC scoring system, the model serves as an independent prognostic factor that provides crucial supplementary molecular stratification. Furthermore, the model underscores the critical roles of energy metabolism and ECM remodeling in NMIBC recurrence, providing a valuable molecular basis for precise individualized management of NMIBC patients in China.

OBJECTIVE:To investigate the expression pattern of Erb-B2 receptor tyrosine kinase 2 (ERBB2) in bladder urothelial carcinoma (BLCA) and its clinical relevance, prognostic value, and potential molecular mechanisms, thereby providing evidence for biomarker identification and targeted therapy research in BLCA. METHODS:RNA sequencing expression data and clinical information were obtained from The Cancer Genome Atlas bladder urothelial carcinoma cohort (TCGA-BLCA). Differences in ERBB2 expression between tumor and normal tissues were analyzed, and associations with American Joint Committee on Cancer (AJCC) pathological stage and tumor grade were evaluated. Receiver operating characteristic (ROC) curve analysis was performed to assess the diagnostic performance of ERBB2. Patients were stratified into high- and low-expression groups based on both the median value and the optimal cutoff, followed by Kaplan-Meier survival analysis and Cox regression to evaluate prognostic significance. Differentially expressed genes associated with ERBB2 were identified, and Kyoto Encyclopedia of Genes and Genomes (KEGG), gene ontology (GO), and single-gene gene set enrichment analysis (GSEA) were conducted. Correlations between ERBB2 and immune checkpoint molecules were further analyzed. In addition, immunohistochemistry data from the Human Protein Atlas (HPA) database and reverse transcription quantitative PCR (RT-qPCR) experiments were used to validate ERBB2 expression. RESULTS:HPA immunohistochemistry demonstrated stronger ERBB2 staining in BLCA neoplastic tissues, and RT-qPCR confirmed elevated ERBB2 mRNA expression in BLCA neoplastic tissues. TCGA analysis showed that ERBB2 expression was significantly higher in tumor tissues than in normal tissues (P=0.005), with overall differences observed across AJCC pathological stages (P=0.004), whereas no significant difference was found between tumor grades (P=0.238). Receiver operating characteristic curve analysis indicated a moderate discriminatory ability of ERBB2 [area under the curve (AUC) =0.689]. No significant difference in overall survival was observed between high- and low-expression groups based on either the median cutoff or the optimal cutoff (P=0.240 and P=0.148, respectively), and both univariate and multivariate Cox analyses suggested that ERBB2 was not an independent prognostic factor for OS. Functional enrichment analyses revealed that ERBB2-associated differentially expressed genes were mainly enriched in cytokine-cytokine receptor interaction, interleukin 17 (IL-17) signaling pathway, phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway, Janus kinase/signal transducer and activator of transcription (JAK-STAT) signaling pathway, chemokine signaling pathway, inflammatory response, immune response, extracellular matrix organization, and leukocyte migration. GSEA further demonstrated positive enrichment in IL-17 signaling, PI3K/AKT signaling, and cytokine-cytokine receptor interaction pathways. Immune checkpoint analysis showed that CD274, PDCD1, CTLA4, LAG3, TIGIT, and HAVCR2 were significantly upregulated in the ERBB2 high-expression group, and ERBB2 expression was positively correlated with CD274 and CTLA4 (Spearman ρ=0.45 and 0.36, both P < 0.001). CONCLUSION:ERBB2 is upregulated in BLCA and is associated with AJCC pathological stage and immune checkpoint expression, showing moderate diagnostic value but limited prognostic significance. ERBB2 may contribute to BLCA progression through regulation of immune-inflammatory responses, cytokine signaling, PI3K/AKT pathway, and tumor immune microenvironment.

Frailty is common in chronic obstructive pulmonary disease (COPD), but the contribution of systemic inflammation to its association with laboratory-based frailty is not fully understood. We examined the relationship between COPD and the frailty index based on laboratory tests (FI-Lab) and explored whether inflammatory markers explained part of this statistical association. Two independent datasets were analyzed, including a hospital-based cohort and the National Health and Nutrition Examination Survey (NHANES). FI-Lab was used to assess frailty. hierarchical linear regression, mediation, sensitivity, and subgroup analyses were performed. COPD was associated with higher FI-Lab in both datasets after adjustment for covariates. Several inflammatory markers explained part of this association statistically. Mediation estimates differed between the two datasets, but the overall pattern was similar. Results changed little in sensitivity analyses. Greater statistical mediation was observed in older participants, those with overweight or obesity, men, and ever-smokers, although these subgroup findings were exploratory. COPD was linked to higher FI-Lab in both datasets. Systemic inflammation may partly underlie this statistical association. Prospective studies are needed to clarify the temporal relationship and the potential clinical usefulness of these inflammatory markers.

Triple-negative breast cancer (TNBC) represents a notably aggressive form of breast cancer, distinguished by heightened invasiveness and an important propensity for metastasis. The expression of ubiquitin D (UBD) is significantly increased in lung metastases associated with TNBC, correlating with unfavorable patient outcomes. Functional assays indicate that UBD promotes invasion, migration, and pulmonary colonization of TNBC cells in vivo. At the mechanistic level, UBD preserves matrix metalloproteinase 3 (MMP3) levels by inhibiting proteasomal degradation. A proteomic analysis has identified MMP3 as a crucial downstream mediator of UBD. Concurrently, chromatin immunoprecipitation and luciferase reporter assays demonstrate that the Spi-B transcription factor (SPIB) directly interacts with the UBD promoter, leading to the activation of its transcription. Collectively, these findings identify the SPIB/UBD/MMP3 axis as a pivotal regulator of TNBC metastasis, indicating its value for prognostic evaluation and targeted therapy.

Dysregulation of fibroblast growth factor receptor (FGFR) signaling contributes to tumorigenesis and FGFRs have been clinically approved as treatment targets for FGFR inhibitor (FGFRi) in urothelial carcinoma (UC). The present study aimed to explore the correlations between different FGFR3 alteration sites and response to FGFRi. We involved a total of 1045 FGF/FGFR-altered UC patients treated with FGFRi, among whom 54.93 % carried FGFR3 mutations and 15.22 % carried FGFR3 fusions. Erdafitinib (47.37 %) was the most frequently used FGFRi drug in clinical studies. The objective response rate was 31.29 % in all participants. Higher frequencies of FGFR3-TACC3 fusion were positively correlated with elevated treatment response rates, particularly in complete response (coefficient=0.762, P = 0.028) and disease control (coefficient=0.786, P = 0.036), whereas FGFR3 S249C mutation showed a negative correlation with response. Similar results were identified in subgroup analyses. In conclusion, UC patients with FGFR3 fusions, especially FGFR3-TACC3 fusions, may benefit more from FGFRi than those with FGFR3 mutations, which highlighted the importance of FGFR3 alteration site test in determining the efficacy of FGFRi-based therapy and enhanced the patient benefit for FGF/FGFR-altered UC. Future studies with larger sample size and individual patient data are needed to confirm these findings and explore the underlying mechanisms of the differential response to FGFRi.

Importance:Medulloblastoma (MB) is the most common malignant brain tumor in children, with metastasis being the primary cause of recurrence and mortality. The tumor microenvironment (TME) plays a critical role in driving metastasis; however, the mechanisms underlying TME alterations in MB metastasis remain poorly understood. Objective:To develop and validate machine learning (ML) models for predicting patient outcomes in MB and to investigate the role of TME components, particularly immune cells and immunoregulatory molecules, in metastasis. Methods:ML models were constructed and validated to predict prognosis and metastasis in MB patients. Eight algorithms were evaluated, and the optimal model was selected. Lasso regression was employed for feature selection, and SHapley Additive exPlanations values were used to interpret the contribution of individual features to model predictions. Immune cell infiltration in tumor tissues was quantified using the microenvironment cell populations-counter method, and immunohistochemistry was applied to analyze the expression and distribution of specific proteins in tumor tissues. Results:The ML models identified metastasis as the strongest predictor of poor prognosis in MB patients, with significantly worse survival outcomes observed in metastatic cases. High infiltration of CD8+ T cells and cytotoxic T lymphocytes (CTLs), along with elevated expression of the TGFB1 gene encoding transforming growth factor beta 1 (TGF-β1), were strongly associated with metastasis. Independent transcriptomic and immunohistochemical analyses confirmed significantly higher CD8+ T cell/CTL infiltration and TGF-β1 expression in metastatic compared to nonmetastatic MB samples. Patients with both high CD8+ T cell/CTL infiltration and elevated TGFB1 expression in the context of metastasis exhibited significantly worse survival outcomes compared to patients with low expression and no metastasis. Interpretation:This study identifies metastasis as the key prognostic factor in MB and reveals the pivotal roles of CD8+ T cells, CTLs, and TGF-β1 within the TME in promoting metastasis and poor outcomes. These findings provide a foundation for developing future therapeutic strategies targeting the TME to improve MB patient outcomes.

Composable visualization is essential in biomedical research, particularly when working with complex, multi-dimensional biological data. However, many existing tools focus on specific fields and lack the comprehensive features needed to capture the intricacies and interrelations of datasets. To address this, we introduce ggalign, an R package built on the grammar of graphics framework, providing an easy-to-use platform for creating composable visualizations of interconnected data. It offers a variety of layout options, including StackLayout, QuadLayout, and CircleLayout, tailored to different data types, and supports flexible multi-dimensional alignments, such as one-to-many, many-to-one, many-to-many, and crosswise relationships. Additionally, ggalign enhances the clarity of visualizations through its annotation features. Overall, ggalign offers a powerful and flexible solution for visualizing complex data in biomedical research. ### Competing Interest Statement The authors have declared no competing interest.

Fibroblast growth factor receptor (FGFR) alteration is one of the common driver alterations in urothelial carcinoma (UC). FGFR alterations contribute to anti-tumor immunity inhibition and are associated with attenuated response to immune checkpoint inhibitor (ICI) or chemotherapy. Selective pan-FGFR tyrosine kinase inhibitor (FGFRi) has been approved for FGFR-altered UC. However, the comparative efficacy and safety of FGFRi with ICI or chemotherapy remains under debate. We analyzed 865 UC patients including 447 with FGFRi and 418 with ICI or chemotherapy. FGFRi showed better recurrence-free survival for non-muscle invasive UC and higher objective response for advanced UC than ICI or chemotherapy. However, FGFRi demonstrated no benefit for the survival of advanced UC and led to more treatment-related adverse events, especially adverse events causing dose interruptions. It is worth noting that patients with liver metastasis might benefit from FGFRi in terms of both prognosis and response. In summary, FGFRi offered higher efficacy and lower safety in second-line treatment of FGFR-altered UC. It is crucial for clinicians to balance the efficacy and safety in different tumor stages when considering the use of FGFRi for UC treatment.

Esophageal squamous cell carcinoma (ESCC) has a poor prognosis, with chemoradiotherapy (CRT) being a key treatment method. This study focused on circulating cytokines as potential predictors of treatment response and prognosis in patients with ESCC. Serum samples were collected from 36 ESCC patients, and 12 different cytokines were quantified using a multiplex immunofluorescence assay. We used non-parametric Wilcoxon unpaired rank tests to examine the relationship between cytokine concentrations and clinical outcomes. The duration of progression-free survival was assessed through imaging studies and telephone follow-ups. Kaplan–Meier survival plots, analyzed with the log-rank test, were utilized to depict survival trends. Pre-treatment serum IL-8 levels were significantly elevated in patients with lymphoid metastases (p = 0.036). Lower initial levels of IL-8 and IL-1β were observed in patients with partial response group compared to those with stable disease (p = 0.002, p = 0.01). Elevated baseline levels of IL-8 and interferon-gamma (IFN-γ) were correlated with a poorer prognosis. Higher levels of IL-5 and IFN-γ levels following therapy were associated with worse outcomes. Our findings indicate that IL-8, IL-1β, IL-5, and IFN-γ may serve as potential biomarkers for treatment efficacy and prognosis in ESCC. Patients with low levels of IL-8 and IL-1β demonstrate a favorable response to CRT. Elevated serum levels of IL-8, IL-1β, IFN-γ, and IL-5 may predict poorer clinical outcomes.

Objective:Many studies have stressed the necessity of repeat transurethral resection (reTURB) following the initial conventional transurethral resection of the bladder for non-muscle invasive bladder cancer (NMIBC) patients. However, there have been few studies focusing on the role of reTURB after en bloc resection of bladder tumor (ERBT) for NMIBC by far. This study aimed to evaluate whether reTURB can be avoided after ERBT. Materials and methods:We conducted research in PubMed, Web of Science, EMBASE, and the Cochrane Library up to November 14, 2024, to identify studies on the reTURB after initial ERBT. For data conversion and the combined calculation of the incidence rate, we utilized R software (R Foundation for Statistical Computing, Vienna, Austria) and Cochrane Review Manager 5.4 (The Cochrane Collaboration, London, UK) along with the double arcsine method. This systematic review protocol was registered at the International Prospective Register of Systematic Reviews (PROSPERO) under number 1082989. Results:A total of 17 studies involving 1051 participants were included. The rates of residual tumor and tumor upstaging detected by reTURB or cystoscopy after ERBT were 9% (95% confidence interval (CI) = 4%-16%) and 0% (95% CI = 0%-1%). No statistically significant positive effect of reTURB after initial ERBT was exhibited in recurrence-free survival (RFS), tumor recurrence, and progression. The pooled hazard ratios of 1-year and 5-year RFS were 0.77 (95% CI = 0.41-1.44, p = 0.41) and 0.83 (95% CI = 0.58-1.20, p = 0.33). The pooled odds ratio of progression and recurrence were 1.13 (95% CI = 0.53-2.41, p = 0.75) and 0.78 (95% CI = 0.53-1.16, p = 0.23). Conclusion:ERBT can successfully regulate the rate of tumor upstaging and residual tumor to an acceptable level. For patients with NMIBC, subsequent reTURB may not be required following the initial ERBT.

Background: Chimeric antigen receptor T-cell (CAR-T) cell therapy represents a significant advancement in cancer treatment, offering remarkable responses in certain hematologic malignancies. However, the risk of secondary primary malignancies (SPMs) associated with CAR-T therapy is a growing concern. Recent studies suggest that antibiotics, which are frequently used in CAR-T patients, may influence this risk, yet their effects remain poorly understood. Objective: This study aims to systematically evaluate the association between antibiotics and the incidence and timing of SPMs in patients receiving CAR-T cell therapy, using data from the FDA’s Adverse Event Reporting System (FAERS) database. Design: We analyzed reports from FAERS spanning from Q2 2017 to Q1 2024, focusing on SPMs associated with various CAR-T therapies. Methods: A comprehensive signal analysis was conducted to explore the associations between antibiotic usage and specific SPMs for different CAR-T products. In addition, we employed cumulative hazard curves to evaluate the time to onset of SPMs in patients receiving antibiotics versus those who did not. Results: We have provided a comprehensive summary of all signals for CAR-T-associated SPMs. In addition, our analysis identified significant variations in the association between antibiotics and SPM incidence depending on the CAR-T therapy administered. Antibiotics were associated with a decreased risk of SPMs in patients treated with anti-CD19 CAR-T therapies, particularly brexucabtagene autoleucel. Conversely, a higher risk of SPMs was observed in association with antibiotics for anti-BCMA therapies, with idecabtagene vicleucel showing a notably elevated risk. Notably, antibiotics were associated with an earlier onset of SPMs across CAR-T therapies, suggesting a possible relationship between antibiotics and the timing of these malignancies. Finally, we explored the underlying biological pathways that may be associated with these observations. Conclusion: Antibiotics were associated with both the risk and timing of SPMs in patients undergoing CAR-T cell therapy. This study highlights the need for further research to better understand the complex interactions between antibiotics and CAR-T therapies, as well as the potential implications for clinical management and patient care.

Background: Immune checkpoint blockade (ICB) has emerged as a promising therapy for both resectable urothelial carcinoma (UC) patients preparing for radical surgery and unresectable UC patients, whereas the objective response rate of ICB remains unsatisfactory due to various factors. Antibiotic (ATB) use can influence intratumoral bacteria, which may further reduce ICB efficacy. The study aims to evaluate the effects of ATB use on prognosis and response in UC patients undergoing ICB, and explore potential molecular mechanisms of ATBs and intratumoral bacteria impacting UC immune microenvironment. Materials and Methods: Pooled analyses, synthesizing evidence from 3496 UC patients with ICB treatment, were conducted. In addition, single-cell RNA and single-cell microbiome data were analyzed based on eight UC samples and 63 185 single cells. Bulk RNA sequencing and clinical data from a single-arm, multicenter, atezolizumab-treated, phase 2 trial, IMvigor210, were used for validation. Results: ATB use exhibited worse overall survival (HR=1.46, 95% CI=[1.20-1.77], P<0.001 and lower objective response (OR=0.43, 95% CI=[0.27-0.68], P<0.001 in UC patients receiving ICB. Single-cell transcriptome and single-cell microbiome analyses identified the presence of intratumoral bacteria was obviously related to elevated antibacterial immune functions; and antibacterial immunity was positively correlated to antitumor immunity in UC immune microenvironment. Intratumoral bacteria could up-regulate CD74-MIF/COPA signaling of immune cells and activation of CD74-MIF/COPA mediated the promotion of T cell antitumor function induced by antibacterial immune cells. UC patients with higher CD74-MIF/COPA signaling carried better overall survival (HR=1.60, 95% CI=[1.19-2.15], P=0.002) in immunotherapy cohort. Conclusion: ATB use reduces overall survival and objective response to ICB in UC patients. Antibacterial immune cell functions induced by intracellular bacteria in the UC microenvironment might up-regulate the function of antitumor T immune cells via activating CD74-MIF/COPA, whereas ATB could inhibit the above process through killing intracellular bacteria and result in poorer clinical benefit of ICB. The use of ATB should be considered carefully during the neoadjuvant immunotherapy period for resectable UC patients preparing for radical surgery and during the immunotherapy period for unresectable UC patients.

The limited genomic data on non-muscle-invasive bladder cancer (NMIBC) hampers our understanding of its carcinogenesis and development. Specifically, Aristolochic acid (AA), a potent human carcinogenic compound from aristolochia plants and commonly found in Chinese herbal medicine, has been extensively documented as being closely associated with the onset and progression of bladder cancer. However, the field of AA-induced NMIBC remains largely unexplored in terms of its genomic and molecular characteristics, as well as clinical therapeutic strategies. To bridge this knowledge gap, we conducted a comprehensive study using a cohort of 81 NMIBC samples. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) to obtain detailed genomic and transcriptomic data. We subjected these datasets to genomic analysis and subtype analysis to gain valuable insights into NMIBC. By temporally dissecting mutations in NMIBC specimens, we identified a comprehensive mutational landscape of NMIBC and the associations of these mutations with recurrence-free survival. Additionally, we discerned four genomic subtypes of NMIBC: AA-like, FGFR3/HRAS, FGFR3 chr9Del, and genome instability (GI). The AA-like subtype presented a high frequency of gene mutations along with a pronounced AA mutagenesis signature of SBS22 (Fisher test: P-value 3.5e-4, OR 25.25) even after temporal dissection. The FGFR3/HRAS subtype exhibited FGFR3 or HRAS mutations with few copy number alterations (CNAs). The FGFR3 chr9Del subtype was characterized by the co-occurrence of chr9p and chr9q deletions as well as FGFR3 mutations, while the GI subtype showed a high frequency of CNAs. Notably, the AA-like and GI subtypes demonstrated better outcomes after immunotherapy, whereas the FGFR3/HRAS subtype showed poorer outcomes. Our findings provide novel perspectives on the genomics of NMIBC, unveiling four prominent genomic subtypes, each showing different outcomes following immunotherapy. Trial registration: No. 2019PHB268-01 (retrospectively registered on February 14, 2020).