BACKGROUND Idiopathic pulmonary fibrosis(IPF)is a progressive interstitial lung disease with a high mortality rate.On this basis,exploring potential therapeutic targets to meet the unmet needs of IPF patients is impor...BACKGROUND Idiopathic pulmonary fibrosis(IPF)is a progressive interstitial lung disease with a high mortality rate.On this basis,exploring potential therapeutic targets to meet the unmet needs of IPF patients is important.AIM To explore novel hub genes for IPF therapy.METHODS Here,we used public datasets to identify differentially expressed genes between IPF patients and healthy donors.Potential targets were considered based on multiple bioinformatics analyses,especially the correlation between hub genes and carbon monoxide diffusing capacity of carbon monoxide,forced vital capacity,and patient survival rate.The mRNA levels of the hub genes were determined through quantitative real-time polymerase chain reaction.RESULTS We found that TDO2 was upregulated in IPF patients and predicted poor prognosis.Surprisingly,single-cell RNA sequencing data analysis revealed significant enrichment of TDO2 in alveolar fibroblasts,indicating that TDO2 may participate in the regulation of proliferation and survival.Therefore,we verified the upregulated expression of TDO2 in an experimental mouse model of transforming growth factor-β(TGF-β)-induced pulmonary fibrosis.Furthermore,the results showed that a TDO2 inhibitor effectively suppressed TGF-β-induced fibroblast activation.These findings suggest that TDO2 may be a potential target for IPF treatment.Based on transcription factors-microRNA prediction and scRNA-seq analysis,elevated TDO2 promoted the IPF proliferation of fibroblasts and may be involved in the P53 pathway and aggravate ageing and persistent pulmonary fibrosis.CONCLUSION We provided new target genes prediction and proposed blocking TGF-βproduction as a potential treatment for IPF.展开更多
Background:Tertiary lymphoid structures(TLSs)promote antitumor immunity and predict favorable immunotherapy outcomes in breast cancer.The study aimed to investigate how Tryptophan 2,3-dioxygenase(TDO2)-associated tryp...Background:Tertiary lymphoid structures(TLSs)promote antitumor immunity and predict favorable immunotherapy outcomes in breast cancer.The study aimed to investigate how Tryptophan 2,3-dioxygenase(TDO2)-associated tryptophan metabolism influences TLS maturation and B cell class switching in breast cancer.Methods:Bulk transcriptomic data from The Cancer Genome Atlas-Breast Invasive Carcinoma(TCGA-BRCA,n=1055)were analyzed using Gene Set Variation Analysis(GSVA)-based metabolic scoring,immune deconvolution,and TLS quantification.Single-cell RNA sequencing(scRNA-seq,n=26)and spatial transcriptomics(n=1)were applied to map TDO2 expression and TLS spatial organization.Validation was performed by immunohistochemistry(n=38)and multiplex immunofluorescence(n=12).Results:We identified that elevated tryptophan metabolism was predominantly enriched in the Luminal A subtype and delineates an immune-cold phenotype with less immunogenicity,associated with a distinct immune-dominant cellular microenvironment,particularly enriched in T and plasma cells.High expression of the tryptophan-metabolizing enzyme TDO2 was significantly enriched in TLS-low tumors and negatively correlated with TLS maturation signatures.Functional enrichment revealed suppressed B cell class switching and attenuated C-X-C motif chemokine ligand 9(CXCL9)expression in TLS-deficient tumors.Spatial transcriptomics and hotspot analysis demonstrated an inverse spatial correlation between TDO2 expression and TLS core components.Tumors with high tryptophan metabolism showed decreased cluster of differentiation 20(CD20)^(+)and CXCL9^(+)cell infiltration within TLS zones.Tumors with strong TDO2-kynurenine activity displayed impaired TLS organization and attenuated humoral immunity.Conditional spatial co-occurrence modeling confirmed reduced proximity between tryptophan metabolism hotspots and TLS-related immune features.Conclusion:In conclusion,our findings suggest that TDO2-associated tryptophan metabolism is linked to impaired TLS maturation and suppressed B cell class switching in breast cancer.Targeting the TDO2-kynurenine axis may represent a promising strategy to restore TLS formation and enhance immunotherapy responsiveness in breast cancer.展开更多
文摘BACKGROUND Idiopathic pulmonary fibrosis(IPF)is a progressive interstitial lung disease with a high mortality rate.On this basis,exploring potential therapeutic targets to meet the unmet needs of IPF patients is important.AIM To explore novel hub genes for IPF therapy.METHODS Here,we used public datasets to identify differentially expressed genes between IPF patients and healthy donors.Potential targets were considered based on multiple bioinformatics analyses,especially the correlation between hub genes and carbon monoxide diffusing capacity of carbon monoxide,forced vital capacity,and patient survival rate.The mRNA levels of the hub genes were determined through quantitative real-time polymerase chain reaction.RESULTS We found that TDO2 was upregulated in IPF patients and predicted poor prognosis.Surprisingly,single-cell RNA sequencing data analysis revealed significant enrichment of TDO2 in alveolar fibroblasts,indicating that TDO2 may participate in the regulation of proliferation and survival.Therefore,we verified the upregulated expression of TDO2 in an experimental mouse model of transforming growth factor-β(TGF-β)-induced pulmonary fibrosis.Furthermore,the results showed that a TDO2 inhibitor effectively suppressed TGF-β-induced fibroblast activation.These findings suggest that TDO2 may be a potential target for IPF treatment.Based on transcription factors-microRNA prediction and scRNA-seq analysis,elevated TDO2 promoted the IPF proliferation of fibroblasts and may be involved in the P53 pathway and aggravate ageing and persistent pulmonary fibrosis.CONCLUSION We provided new target genes prediction and proposed blocking TGF-βproduction as a potential treatment for IPF.
基金supported by grants from the Beijing Xisike Clinical Oncology Research Foundation(No.Y-Young2024-0138)China Postdoctoral Science Foundation(No.2024M750538)Qingdao Chengyang People’s Hospital Fund Project(No.202510300).
文摘Background:Tertiary lymphoid structures(TLSs)promote antitumor immunity and predict favorable immunotherapy outcomes in breast cancer.The study aimed to investigate how Tryptophan 2,3-dioxygenase(TDO2)-associated tryptophan metabolism influences TLS maturation and B cell class switching in breast cancer.Methods:Bulk transcriptomic data from The Cancer Genome Atlas-Breast Invasive Carcinoma(TCGA-BRCA,n=1055)were analyzed using Gene Set Variation Analysis(GSVA)-based metabolic scoring,immune deconvolution,and TLS quantification.Single-cell RNA sequencing(scRNA-seq,n=26)and spatial transcriptomics(n=1)were applied to map TDO2 expression and TLS spatial organization.Validation was performed by immunohistochemistry(n=38)and multiplex immunofluorescence(n=12).Results:We identified that elevated tryptophan metabolism was predominantly enriched in the Luminal A subtype and delineates an immune-cold phenotype with less immunogenicity,associated with a distinct immune-dominant cellular microenvironment,particularly enriched in T and plasma cells.High expression of the tryptophan-metabolizing enzyme TDO2 was significantly enriched in TLS-low tumors and negatively correlated with TLS maturation signatures.Functional enrichment revealed suppressed B cell class switching and attenuated C-X-C motif chemokine ligand 9(CXCL9)expression in TLS-deficient tumors.Spatial transcriptomics and hotspot analysis demonstrated an inverse spatial correlation between TDO2 expression and TLS core components.Tumors with high tryptophan metabolism showed decreased cluster of differentiation 20(CD20)^(+)and CXCL9^(+)cell infiltration within TLS zones.Tumors with strong TDO2-kynurenine activity displayed impaired TLS organization and attenuated humoral immunity.Conditional spatial co-occurrence modeling confirmed reduced proximity between tryptophan metabolism hotspots and TLS-related immune features.Conclusion:In conclusion,our findings suggest that TDO2-associated tryptophan metabolism is linked to impaired TLS maturation and suppressed B cell class switching in breast cancer.Targeting the TDO2-kynurenine axis may represent a promising strategy to restore TLS formation and enhance immunotherapy responsiveness in breast cancer.
