Arabis stelleri var. japonica evidenced stronger osmotic stress tolerance than Arabidopsis thaliana. Using an A. thaliana microarray chip, we determined changes in the expression of approximately 2 800 genes between A...Arabis stelleri var. japonica evidenced stronger osmotic stress tolerance than Arabidopsis thaliana. Using an A. thaliana microarray chip, we determined changes in the expression of approximately 2 800 genes between A. stelleri plants treated with 0.2 M mannitol versus mock-treated plants. The most significant changes in the gene expression patterns were in genes defining cellular components or in genes associated with the endomembrane system, stimulus response, stress response, chemical stimulus response, and defense response. The expression patterns of three de novo proline biosynthesis enzymes were evaluated in A. stelleri var. japonica seedlings treated with 0.2 M mannitol, 0.2 M sorbitol, and 0.2 M NaCI. The expression of At-pyrroline-5-carboxylate synthetase was not affected by NaCI stress but was similarly induced by mannitol and sorbitol. The proline dehydrogenase gene, which is known to be repressed by dehydration stress and induced by free L-proline, was induced at an early stage by mannitol treatment, but the level of proline dehydrogenase was increased later by treatment with both mannitol and NaCI. The level of free L-proline accumulation increased progressively in response to treatments with mannitol, sorbitol, and NaCI. Mannitol induced L-proline accumulation more rapidly than NaCI or sorbitol. These findings demonstrate that the osmotic tolerance of the novel halophyte, Arabis stelleri, is associated with the accumulation of L-proline.展开更多
Background and Aims:Targeted therapy and immunotherapy have emerged as treatment options for hepatocellular carcinoma(HCC)in recent years.The significance of serine and glycine metabolism in various cancers is widely ...Background and Aims:Targeted therapy and immunotherapy have emerged as treatment options for hepatocellular carcinoma(HCC)in recent years.The significance of serine and glycine metabolism in various cancers is widely acknowledged.This study aims to investigate their correlation with the prognosis and tumor immune microenvironment(TIME)of HCC.Methods:Based on the public database,different subtypes were identified by cluster analysis,and the prognostic model was constructed through regression analysis.The gene expression omnibus(GEO)data set was used as the validation set to verify the performance of the model.The survival curve evaluated prognostic ability.CIBERSORT was used to evaluate the level of immune cell infiltration,and maftools analyzed the mutations.DsigDB screened small molecule compounds related to prognostic genes.Results:HCC was found to have two distinct subtypes.Subsequently,we constructed a risk score prognostic model through regression analysis based on serine and glycine metabolismrelated genes(SGMGs).A nomogram was constructed based on risk scores and other clinical factors.HCC patients with a higher risk score showed a poor prognosis,and there were significant differences in immune cell infiltration between the high-and low-risk groups.In addition,three potential drugs associated with prognostic genes,streptozocin,norfloxacin,and hydrocotarnine,were identified.Conclusions:This study investigated the expression patterns of SGMGs and their relationship with tumor characteristics,resulting in the development of a novel model for predicting the prognosis of HCC patients.The study provides a reference for clinical prognosis prediction and treatment of HCC patients.展开更多
BACKGROUND Stomach adenocarcinoma(STAD)is a leading cause of cancer deaths,but its molecular and prognostic characteristics has never been fully illustrated.AIM To describe a molecular evaluation of primary STAD and d...BACKGROUND Stomach adenocarcinoma(STAD)is a leading cause of cancer deaths,but its molecular and prognostic characteristics has never been fully illustrated.AIM To describe a molecular evaluation of primary STAD and develop new therapies and identify promising prognostic signatures.METHODS We describe a comprehensive molecular evaluation of primary STAD based on comprehensive analysis of energy-metabolism-related gene(EMRG)expression profiles.RESULTS On the basis of 86 EMRGs that were significantly associated to patients’progression-free survival(PFS),we propose a molecular classification dividing gastric cancer into two subtypes:Cluster 1,most of which are young patients and display more immune and stromal cell components in tumor microenvironment and lower tumor priority;and Cluster 2,which show early stages and better PFS.Moreover,we construct a 6-gene signature that can classify the prognostic risk of patients after a three-phase training test and validation process.Compared with patients with low-risk score,patients with high-risk score had shorter overall survival.Furthermore,calibration and DCA analysis plots indicate the excellent predictive performance of the 6-gene signature,and which present higher robustness and clinical usability compared with three previous reported prognostic gene signatures.According to gene set enrichment analysis,gene sets related to the high-risk group were participated in the ECM receptor interaction and hedgehog signaling pathway.CONCLUSION Identification of the EMRG-based molecular subtypes and prognostic gene model provides a roadmap for patient stratification and trials of targeted therapies.展开更多
基金supported by a grant from the Cooperative Research Projects for Bioenergy Crop Development RDA (RIMS20070201036026)
文摘Arabis stelleri var. japonica evidenced stronger osmotic stress tolerance than Arabidopsis thaliana. Using an A. thaliana microarray chip, we determined changes in the expression of approximately 2 800 genes between A. stelleri plants treated with 0.2 M mannitol versus mock-treated plants. The most significant changes in the gene expression patterns were in genes defining cellular components or in genes associated with the endomembrane system, stimulus response, stress response, chemical stimulus response, and defense response. The expression patterns of three de novo proline biosynthesis enzymes were evaluated in A. stelleri var. japonica seedlings treated with 0.2 M mannitol, 0.2 M sorbitol, and 0.2 M NaCI. The expression of At-pyrroline-5-carboxylate synthetase was not affected by NaCI stress but was similarly induced by mannitol and sorbitol. The proline dehydrogenase gene, which is known to be repressed by dehydration stress and induced by free L-proline, was induced at an early stage by mannitol treatment, but the level of proline dehydrogenase was increased later by treatment with both mannitol and NaCI. The level of free L-proline accumulation increased progressively in response to treatments with mannitol, sorbitol, and NaCI. Mannitol induced L-proline accumulation more rapidly than NaCI or sorbitol. These findings demonstrate that the osmotic tolerance of the novel halophyte, Arabis stelleri, is associated with the accumulation of L-proline.
基金supported by Postgraduate Science Foundation Project of Zhejiang Chinese Medical University(No.Y202248712).
文摘Background and Aims:Targeted therapy and immunotherapy have emerged as treatment options for hepatocellular carcinoma(HCC)in recent years.The significance of serine and glycine metabolism in various cancers is widely acknowledged.This study aims to investigate their correlation with the prognosis and tumor immune microenvironment(TIME)of HCC.Methods:Based on the public database,different subtypes were identified by cluster analysis,and the prognostic model was constructed through regression analysis.The gene expression omnibus(GEO)data set was used as the validation set to verify the performance of the model.The survival curve evaluated prognostic ability.CIBERSORT was used to evaluate the level of immune cell infiltration,and maftools analyzed the mutations.DsigDB screened small molecule compounds related to prognostic genes.Results:HCC was found to have two distinct subtypes.Subsequently,we constructed a risk score prognostic model through regression analysis based on serine and glycine metabolismrelated genes(SGMGs).A nomogram was constructed based on risk scores and other clinical factors.HCC patients with a higher risk score showed a poor prognosis,and there were significant differences in immune cell infiltration between the high-and low-risk groups.In addition,three potential drugs associated with prognostic genes,streptozocin,norfloxacin,and hydrocotarnine,were identified.Conclusions:This study investigated the expression patterns of SGMGs and their relationship with tumor characteristics,resulting in the development of a novel model for predicting the prognosis of HCC patients.The study provides a reference for clinical prognosis prediction and treatment of HCC patients.
基金the National Natural Science Foundation of China,No.81972249,No.81802367,No.81802361 and No.82172702the Shanghai Clinical Research Plan of SHDC,No.SHDC2020CR4068+3 种基金the Shanghai Clinical Science and Technology Innovation Project of Municipal Hospital,No.SHDC12020102the Shanghai Science and Technology Development Fund,No.18ZR1408000,No.21ZR1414900 and No.19MC1911000the Clinical Research Project of Shanghai Municipal Health Committee,No.20194Y0348and the Shanghai“Rising Stars of Medical Talents”Youth Development Program Youth Medical Talents–Specialist Program,No.SHWSRS(2020)_087.
文摘BACKGROUND Stomach adenocarcinoma(STAD)is a leading cause of cancer deaths,but its molecular and prognostic characteristics has never been fully illustrated.AIM To describe a molecular evaluation of primary STAD and develop new therapies and identify promising prognostic signatures.METHODS We describe a comprehensive molecular evaluation of primary STAD based on comprehensive analysis of energy-metabolism-related gene(EMRG)expression profiles.RESULTS On the basis of 86 EMRGs that were significantly associated to patients’progression-free survival(PFS),we propose a molecular classification dividing gastric cancer into two subtypes:Cluster 1,most of which are young patients and display more immune and stromal cell components in tumor microenvironment and lower tumor priority;and Cluster 2,which show early stages and better PFS.Moreover,we construct a 6-gene signature that can classify the prognostic risk of patients after a three-phase training test and validation process.Compared with patients with low-risk score,patients with high-risk score had shorter overall survival.Furthermore,calibration and DCA analysis plots indicate the excellent predictive performance of the 6-gene signature,and which present higher robustness and clinical usability compared with three previous reported prognostic gene signatures.According to gene set enrichment analysis,gene sets related to the high-risk group were participated in the ECM receptor interaction and hedgehog signaling pathway.CONCLUSION Identification of the EMRG-based molecular subtypes and prognostic gene model provides a roadmap for patient stratification and trials of targeted therapies.
