TRIM28 is required for SLC27A1 expression.

S. pneumoniae promotes metabolic reprogramming and enhances pazopanib tolerance in ccRCC cells.

S. pneumoniae has no effect on endothelial cell survival or angiogenesis upon pazopanib treatment.

The primers sequences used for ChIP-qPCR

The primers sequences used for qRT-PCR

Distinct bacterial community diversity between PAZ-S and PAZ-R samples.

Summary of clinical ccRCC patients

Currently, there is a lack of precise instruments for predicting the prognosis and treatment efficacy of kidney renal clear cell carcinoma (KIRC), often resulting in delayed diagnosis and suboptimal treatment outcomes. De novo lipogenesis (DNL) has been documented to significantly impact the prognosis and treatment of several cancers and may serve as a biomarker for KIRC treatment and outcomes. We utilized TCGA-KIRC as the training cohort and GSE22541, ematb1980, and emtab3267 as validation cohorts to construct prognostic genetic features (DPGS) for DNL using StepCox[backward] + RSF. We confirmed the independent prognostic value of DPGS through multivariate Cox analysis and integrated DPGS with clinical characteristics to construct comprehensive prognostic nomograms. Furthermore, we analyzed the correlations between DPGS and genomic instability, tumor immune microenvironment (TIME), and immunotherapy sensitivity at both the single-cell and RNA-seq levels. These findings were further validated in the GSE78220, IMvigor210, and Checkmate immunotherapy cohorts. Finally, we used immunohistochemistry (IHC), Western blotting (WB), and cell function assays to elucidate SLC19A1’s critical role in KIRC. The composite C-index for DPGS was 0.796, with hazard ratio (HR) values in multivariate Cox regression analyses of 1.06 and 1.01 in the TCGA-KIRC and EMTAB1980 datasets, respectively. These findings suggest that DPGS can function as an independent prognostic risk factor. Furthermore, the area under the curve (AUC) values for DPGS at 2, 3, and 5 years exceeded 0.67 across four cohorts, indicating robust prognostic predictive performance. In addition, DPGS exhibited a significant association with copy number variation (CNV) (R = 0.33, P < 0.001) and tumor mutational burden (TMB) (R = 0.19, P < 0.001). DPGS was found to accumulate in tumor epithelial cells, cancer-associated fibroblasts (CAFs), and macrophages, and acted on effector CD8 T cells via the HLA-E – KLRC1/NKG2A pathway, thereby diminishing immunotherapy sensitivity in the high-risk DPGS group. Furthermore, knockdown of the key gene SLC19A1 further reduced lipid storage in KIRC and mitigated the malignant phenotype. Our work underscores the critical role of DPGS in modulating TIME, influencing immunotherapy response, and predicting prognosis in KIRC. The integration of DPGS and nomograms based on DNL provides innovated insights into survival prediction and therapy, contributing to the development of DNL-targeted therapeutic strategies.

5 differentially bound transcription factors

S. pneumoniae influences lipid metabolism reprogramming in ccRCC cells by activating SLC27A1 expression.

The details of primary antibodies used for western blot, ChIP, immunoprecipitation, immunohistochemistry and immunofluorescence

Fatty acid metabolism-related pathways in GSEA analysis

S. pneumoniae–mediated pazopanib resistance in ccRCC xenografts requires psaA.

SP1 regulates the transcription of SLC27A1.

Proteins with increased S-nitrosylation levels following Mn2+ treatment

Persistent drug resistance to tyrosine kinase inhibitors (TKI) has become a hurdle in extending the survival of patients with clear cell renal cell carcinoma (ccRCC). Through microbiome screening of patient samples from a ccRCC cohort treated with the TKI pazopanib, we identified Streptococcus pneumoniae as the dominant intratumoral microbiota in pazopanib-resistant ccRCC samples. Further investigation revealed that S. pneumoniae reprogrammed lipid metabolism in ccRCC cells by depleting manganese (Mn2+) from the tumor microenvironment, consequently facilitating malignant progression and development of pazopanib resistance. S. pneumoniae suppressed S-nitrosylation of tripartite motif-containing protein 28 (TRIM28) by diminishing Mn2+ levels, allowing TRIM28 to physically interact with the transcription factor SP1 to promote the transcription of solute carrier family 27 member 1 (SLC27A1) and lipid deposition. Taken together, these findings indicate that tumor-resident S. pneumoniae plays an important role in conferring pazopanib resistance, suggesting that S. pneumoniae could serve as a potential biomarker of pazopanib response in ccRCC.Significance: Streptococcus pneumoniae is an intratumoral bacteria that drives pazopanib resistance in renal cell carcinoma, highlighting the potential of targeting the tumor microbiome as a strategy to improve treatment outcomes in cancer patients.

Cutibacterium and S. vestibularis fail to confer pazopanib resistance in ccRCC cells.

Gender related differences in the occurrence and progression of bladder cancer are affected by sex hormones and their receptor signaling pathways. Angiogenesis inhibitors targeting vascular endothelial growth factor do not show therapeutic effectiveness in bladder cancer patients. In this study, we found that the expression of ERα is positively correlated with vascular mimicry (VM) formation as well as the infiltration of M2 type tumor associated macrophages (TAM). However, it is unclear how this connection between ERα and macrophages affects VM and its detailed mechanism. Our in vitro results showed that macrophage-induced upregulation of ERα promotes VM in BLCA cells by transcriptionally upregulating CDH5. Further research has found that upregulated ERα in BLCA cells induces polarization of M2 macrophages by activating the PTEN/PI3K/pAKT pathway through exosomes derived from tumor cells. Mechanistic investigations have revealed that exosomal miR-642a-5p upregulated by ERα in BLCA cells downregulate PTEN expression in macrophages by directly targeting the 3’UTR of PTEN mRNA. Preclinical experiments involving in vitro BLCA cell lines and an in vivo mouse xenograft model confirm this newly identified pathway and its feedback circuit, offering new perspectives for the development of innovative treatment strategies for BLCA.

Bladder cancer (BCa) is the most prevalent cancer of the urinary system in adults; the prognosis is dismal for BCa treated with gemcitabine (GEM) owing to intrinsic or acquired chemoresistance. This study investigated the potential of Qici Sanling decoction (QCSL), an herbal Chinese medicine, to augment the efficacy of GEM in treating GEM-resistant BCa via network pharmacology and RNA sequencing. We screened 103 active components of QCSL and their 226 targets from the TCMSP database and identified 3985 targets of GEM-resistant BCa via transcriptome sequencing. On the basis of the 69 common targets, a proteinprotein interaction (PPI) network was constructed to identify the top 7 targets. Disease Ontology (DO), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses were conducted to uncover key pathways. CCK-8 assays, Western blotting, flow cytometry, colony formation, and EdU assays were used to assess the apoptosis and proliferation of GEM-resistant T24 and J82 cells treated with QCSL. The BCa gene set was among the top enriched gene sets in the DO analysis; GO analysis revealed enrichment of 2020 terms linked to GEM resistance, and KEGG analysis revealed 161 enriched signalling pathways. Molecular docking indicated that PTGS2 has high affinity for targets of QCSL components. In vitro experiments demonstrated that cells treated with both QCSL and GEM had significantly reduced viability, increased levels of apoptosis, and decreased proliferative capacity. Thus, QCSL enhances the therapeutic effects of GEM in BCa by promoting cell apoptosis and inhibiting cell proliferation. These findings have significant clinical implications, highlighting a potential combined treatment strategy for GEM-resistant BCa to improve patient outcomes.