Lung cancer is a prevalent malignancy,and fatalities of the disease exceed 400,000 cases worldwide.Lung squamous cell carcinoma(LUSC)has been recognized as the most common pathological form of lung cancer.The comprehe...Lung cancer is a prevalent malignancy,and fatalities of the disease exceed 400,000 cases worldwide.Lung squamous cell carcinoma(LUSC)has been recognized as the most common pathological form of lung cancer.The comprehensive understanding of molecular features related to LUSC progression has great significance in LUSC prognosis assessment and clinical management.In this study,we aim to identify a panel of signature genes closely associated with LUSC,which can provide novel insights into the progression of LUSC.Gene expression profiles were retrieved from public resources including gene expression omnibus(GEO)and the cancer genome atlas(TCGA)database.Differentially expressed genes(DEGs)between LUSC specimens and normal lung tissues were identified by bioinformatics analyses.A total of 66 DEGs were identified based on two cohorts of data.CytoHubba plugin of Cytoscape software was utilized for the further analyses of the top 10 candidate hub genes including OGN,ABI3BP,MAMDC2,FGF7,FAM107A,SPARCL1,DCN,COL14A1,and MFAP4 and CHRDL1,which showed significant downregulation in LUSC.Two LUSC cell lines were used to validate the functions of CHRDL1 and FAM107A through overexpression experiment.Together,our data revealed novel candidate tumor-suppressor genes in LUSC,suggesting previously unappreciated mechanisms in the progression of LUSC.展开更多
【目的】鉴定筛选出与疣吻沙蚕性腺发育相关的候选基因及信号通路,揭示其性别分化及变态的分子调控机制,为疣吻沙蚕大规模人工繁育技术的突破提供理论依据。【方法】以成熟雄性(M)、成熟雌性(F)和未变态疣吻沙蚕(R)为研究对象,通过Illum...【目的】鉴定筛选出与疣吻沙蚕性腺发育相关的候选基因及信号通路,揭示其性别分化及变态的分子调控机制,为疣吻沙蚕大规模人工繁育技术的突破提供理论依据。【方法】以成熟雄性(M)、成熟雌性(F)和未变态疣吻沙蚕(R)为研究对象,通过Illumina NovaSeq 6000平台完成高通量转录组测序,经过滤、质量控制及拼接组装后,依据FoldChange≥2且错误发现率(FDR)<0.01的筛选标准,通过DESeq2筛选出差异表达基因(DEGs),然后进行GO功能注释分析和KEGG信号通路富集分析,并以实时荧光定量PCR对转录组测序结果进行验证。【结果】经转录组测序从9个疣吻沙蚕样品中获得46891条Unigenes,在COG、GO、KEGG、KOG、Pfam、Swiss-Prot、TrEMBL、eggNOG和Nr等9个主要功能数据库中有27878条Unigenes得到注释。依据筛选标准,共筛选出1798个DEGs,其中,M vs F组有349个DEGs,R vs F组有1090个DEGs,R vs M组有359个DEGs。GO功能注释分析发现,DEGs主要注释到细胞、细胞部分、结合、细胞过程、单生物过程等GO功能条目;KEGG信号通路富集分析结果表明,DEGs主要富集在氧化磷酸化、花生四烯酸代谢、视黄醇代谢、甘氨酸/丝氨酸/苏氨酸代谢等信号通路上。综合DEGs的KEGG信号通路富集分析及Nr数据库BLASTx比对分析,最终筛选出DMRT1、SOX7、HSP90、CALM等14个与疣吻沙蚕性腺发育相关的DEGs。实时荧光定量PCR检测的目的基因表达趋势与转录组测序分析结果基本一致,进一步证实转录组测序结果的准确性。【结论】疣吻沙蚕的性腺发育和成熟机制与多基因发挥功能及多个信号通路相关,包括雄性个体偏向MT-CYB、HSP60和DNAH5等基因,雌性个体偏向HSP90、SOX7和COL1A1等基因,以及氧化磷酸化、花生四烯酸代谢、视黄醇代谢、甘氨酸/丝氨酸/苏氨酸代谢等与性腺发育相关的信号通路。展开更多
Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 t...Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,respectively.Secondly,shelf-life analysis was carried out for both cultivars at room temperature.Results exhibited that Riogrand showed higher firmness and less weight loss than SalarF1.The ethylene production was higher in SalarF1,compared with Riogrand during post-harvest storages.We performed transcriptomic analysis of both cultivars in different storage stages.We discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),respectively.These genes are enriched in ethylene biosynthesis and response,as well as cell wall-related genes.Ethylene response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in SalarF1.Regarding cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of SalarF1.The quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome analysis.The findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes.展开更多
Background: Fusobacterium nucleatum can cause opportunistic and chronic infections and has recently been shown to be involved in colorectal cancer. However, the specific mechanism by which F. nucleatum induces colorect...Background: Fusobacterium nucleatum can cause opportunistic and chronic infections and has recently been shown to be involved in colorectal cancer. However, the specific mechanism by which F. nucleatum induces colorectal carcinoma remains unclear. Methods: We downloaded the GSE110223, GSE110224, GSE113513 and GSE122183 microarray datasets from the Gene Expression Omnibus (GEO) database. Identification of differentially expressed genes (DEGs) related to F. nucleatum in CRC by overlapping data sets was performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome pathway (KEGG) analyses were used for enrichment analysis. Moreover, Cytoscape software constructed a protein-protein interaction (PPI) network of differentially expressed genes. Finally, western blot and RT-qPCR analysis identified the relative protein and mRNA expression of hub genes in the cell model. Results: In total, 118 DEGs in F. nucleatum-associated CRC were screened from nonoverlapping microarray data, among which 20 upregulated and 98 downregulated DEGs were identified. The 118 DEGs were significantly correlated with diverse functions and pathways. The hub gene MUC1 had higher centrality scores in the PPI network, and the top 5 closely interacting hub genes, SLC7A11, AGR2, KRT18, CARTPT and TSPYL5, were identified. Conclusion: Our evidence suggests that the identified DEGs associated with F. nucleatum enhance our comprehension of the molecular Mechanisms underlying the tumorigenesis and development of CRC and might be used as molecular targets and diagnostic biomarkers for the treatment of CRC.展开更多
目的:研究癫痫对C57小鼠脑组织海马区小胶质细胞极化后基因的富集分析。方法:将40只C57小鼠利用随机分组的方法随机分为对照组(CNC组12只)和癫痫组(OPTZ组28只)。CNC组每隔一天腹腔注射生理盐水,OPTZ组每隔一天腹腔注射戊四唑,共28天。...目的:研究癫痫对C57小鼠脑组织海马区小胶质细胞极化后基因的富集分析。方法:将40只C57小鼠利用随机分组的方法随机分为对照组(CNC组12只)和癫痫组(OPTZ组28只)。CNC组每隔一天腹腔注射生理盐水,OPTZ组每隔一天腹腔注射戊四唑,共28天。在诱导癫痫的实验过程中,观察小鼠的日常行为、癫痫发作程度、癫痫持续时间和癫痫发作后的结局。实验结束后采集样本,进行转录组测序分析。OE生物技术有限公司(上海,中国)负责样品Methylation EPIC Bead Chip实验结果和数据分析的进行。结果:转录组相关测序显示癫痫发作改变小鼠脑组织海马区小胶质细胞M2型的基因表达,其中表达上调基因245个,表达下调基因88个,GO富集分析显示上调基因富集于影响小胶质细胞生长和增殖的通路。结论:癫痫发作改变小鼠海马区小胶质细胞的基因表达且富集于抑制小胶质细胞生长发育通路。Objective: To study the gene enrichment of microglia in hippocampal region of C57 mouse brain after polarization induced by epilepsy. Methods: 40 C57 mice were randomly divided into control group (12 in CNC group) and epilepsy group (28 in OPTZ group). The CNC group was intraperitoneally injected with normal saline every other day, and the OPTZ group was intraperitoneally injected with pentatetrazole every other day for 28 days. In the course of the experiment to induce epilepsy, the daily behavior of the mouse, the degree of seizure, the duration of seizure and the outcome after seizure were observed. After the experiment, the samples were collected and analyzed by transcriptome sequencing. OE Biotechnology Co. Ltd. (Shanghai, China) was responsible for the experimental results and data analysis of the sample, Methylation EPIC Bead Chip. Results: Transcriptome sequencing showed that seizures changed the M2 gene expression of microglia in the hippocampus of mouse brain tissue, including 245 up-regulated genes and 88 down-regulated genes. GO enrichment analysis showed that up-regulated genes were enriched in the pathway affecting the growth and proliferation of microglia. Conclusion: Epileptic seizure changes the gene expression of microglia in the hippocampus of mouse and is concentrated in the pathway that inhibits the growth and development of microglia.展开更多
Sebastiscus marmoratus is one of the ideal fish species for offshore breeding,and temperature changes directly affect its physiological process.We performed whole-transcriptome sequencing of the liver tissues of S.mar...Sebastiscus marmoratus is one of the ideal fish species for offshore breeding,and temperature changes directly affect its physiological process.We performed whole-transcriptome sequencing of the liver tissues of S.marmoratus under heat stress(25℃),normal condition(20℃,the control),and cold stress(15℃).A total of 376 differentially expressed genes(DEGs),147 differentially expressed lncRNAs(DELs),and 40 differentially expressed miRNAs(DEMis)were detected under heat stress;59 DEGs,59 DELs,and 44 DEMis were detected under cold stress.Furthermore,a competing endogenous RNA regulatory network for the functional interaction of lncRNA-miRNA-mRNA was constructed,and GO and KEGG enrichment analyses showed that genes involved in maintaining homeostasis or adjusting to stress and stimulation were strongly activated during heat stress.Including heat-shock protein-related genes Hsp70,FKBP4,and Hspa4a regulated by dre-mir-205-5p;energy metabolism-related genes GCK,g6pca,and RFK regulated by dre-miR-205-5p,dre-miR-145-5p,novel_441,TCONS_00023692,and tcon_00095578;and immune-related genes SCAF,NLRC3,per1b,herc4,MafG,and KLHL29 regulated by dre-miR-456,novel_640,novel_163,TCONS_00079377,TCONS_00063590,and TCONS_000605708.Our findings provide new insights into the adaptation of S.marmoratus to acute temperature changes.展开更多
基金Department of Science and Technology of Yunnan Province,Provincial Basic Research Program(Kunkun-Medical Joint Special Project),202101AY070001-134Yunnan Provincial Department of Science and Technology,Yunnan Provincial Gerontology Research Center,202102AA310069Yunnan Provincial Department of Science and Technology-Kunming Medical University Basic Research Joint Special Key Project,202201AY070001-136.
文摘Lung cancer is a prevalent malignancy,and fatalities of the disease exceed 400,000 cases worldwide.Lung squamous cell carcinoma(LUSC)has been recognized as the most common pathological form of lung cancer.The comprehensive understanding of molecular features related to LUSC progression has great significance in LUSC prognosis assessment and clinical management.In this study,we aim to identify a panel of signature genes closely associated with LUSC,which can provide novel insights into the progression of LUSC.Gene expression profiles were retrieved from public resources including gene expression omnibus(GEO)and the cancer genome atlas(TCGA)database.Differentially expressed genes(DEGs)between LUSC specimens and normal lung tissues were identified by bioinformatics analyses.A total of 66 DEGs were identified based on two cohorts of data.CytoHubba plugin of Cytoscape software was utilized for the further analyses of the top 10 candidate hub genes including OGN,ABI3BP,MAMDC2,FGF7,FAM107A,SPARCL1,DCN,COL14A1,and MFAP4 and CHRDL1,which showed significant downregulation in LUSC.Two LUSC cell lines were used to validate the functions of CHRDL1 and FAM107A through overexpression experiment.Together,our data revealed novel candidate tumor-suppressor genes in LUSC,suggesting previously unappreciated mechanisms in the progression of LUSC.
文摘【目的】鉴定筛选出与疣吻沙蚕性腺发育相关的候选基因及信号通路,揭示其性别分化及变态的分子调控机制,为疣吻沙蚕大规模人工繁育技术的突破提供理论依据。【方法】以成熟雄性(M)、成熟雌性(F)和未变态疣吻沙蚕(R)为研究对象,通过Illumina NovaSeq 6000平台完成高通量转录组测序,经过滤、质量控制及拼接组装后,依据FoldChange≥2且错误发现率(FDR)<0.01的筛选标准,通过DESeq2筛选出差异表达基因(DEGs),然后进行GO功能注释分析和KEGG信号通路富集分析,并以实时荧光定量PCR对转录组测序结果进行验证。【结果】经转录组测序从9个疣吻沙蚕样品中获得46891条Unigenes,在COG、GO、KEGG、KOG、Pfam、Swiss-Prot、TrEMBL、eggNOG和Nr等9个主要功能数据库中有27878条Unigenes得到注释。依据筛选标准,共筛选出1798个DEGs,其中,M vs F组有349个DEGs,R vs F组有1090个DEGs,R vs M组有359个DEGs。GO功能注释分析发现,DEGs主要注释到细胞、细胞部分、结合、细胞过程、单生物过程等GO功能条目;KEGG信号通路富集分析结果表明,DEGs主要富集在氧化磷酸化、花生四烯酸代谢、视黄醇代谢、甘氨酸/丝氨酸/苏氨酸代谢等信号通路上。综合DEGs的KEGG信号通路富集分析及Nr数据库BLASTx比对分析,最终筛选出DMRT1、SOX7、HSP90、CALM等14个与疣吻沙蚕性腺发育相关的DEGs。实时荧光定量PCR检测的目的基因表达趋势与转录组测序分析结果基本一致,进一步证实转录组测序结果的准确性。【结论】疣吻沙蚕的性腺发育和成熟机制与多基因发挥功能及多个信号通路相关,包括雄性个体偏向MT-CYB、HSP60和DNAH5等基因,雌性个体偏向HSP90、SOX7和COL1A1等基因,以及氧化磷酸化、花生四烯酸代谢、视黄醇代谢、甘氨酸/丝氨酸/苏氨酸代谢等与性腺发育相关的信号通路。
基金supported by the National Natural Science Foundation of China(Grant No.U23A20204)the“Wanjiang Scholar Program(Anhui Province)”.
文摘Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,respectively.Secondly,shelf-life analysis was carried out for both cultivars at room temperature.Results exhibited that Riogrand showed higher firmness and less weight loss than SalarF1.The ethylene production was higher in SalarF1,compared with Riogrand during post-harvest storages.We performed transcriptomic analysis of both cultivars in different storage stages.We discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),respectively.These genes are enriched in ethylene biosynthesis and response,as well as cell wall-related genes.Ethylene response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in SalarF1.Regarding cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of SalarF1.The quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome analysis.The findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes.
文摘Background: Fusobacterium nucleatum can cause opportunistic and chronic infections and has recently been shown to be involved in colorectal cancer. However, the specific mechanism by which F. nucleatum induces colorectal carcinoma remains unclear. Methods: We downloaded the GSE110223, GSE110224, GSE113513 and GSE122183 microarray datasets from the Gene Expression Omnibus (GEO) database. Identification of differentially expressed genes (DEGs) related to F. nucleatum in CRC by overlapping data sets was performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome pathway (KEGG) analyses were used for enrichment analysis. Moreover, Cytoscape software constructed a protein-protein interaction (PPI) network of differentially expressed genes. Finally, western blot and RT-qPCR analysis identified the relative protein and mRNA expression of hub genes in the cell model. Results: In total, 118 DEGs in F. nucleatum-associated CRC were screened from nonoverlapping microarray data, among which 20 upregulated and 98 downregulated DEGs were identified. The 118 DEGs were significantly correlated with diverse functions and pathways. The hub gene MUC1 had higher centrality scores in the PPI network, and the top 5 closely interacting hub genes, SLC7A11, AGR2, KRT18, CARTPT and TSPYL5, were identified. Conclusion: Our evidence suggests that the identified DEGs associated with F. nucleatum enhance our comprehension of the molecular Mechanisms underlying the tumorigenesis and development of CRC and might be used as molecular targets and diagnostic biomarkers for the treatment of CRC.
文摘目的:研究癫痫对C57小鼠脑组织海马区小胶质细胞极化后基因的富集分析。方法:将40只C57小鼠利用随机分组的方法随机分为对照组(CNC组12只)和癫痫组(OPTZ组28只)。CNC组每隔一天腹腔注射生理盐水,OPTZ组每隔一天腹腔注射戊四唑,共28天。在诱导癫痫的实验过程中,观察小鼠的日常行为、癫痫发作程度、癫痫持续时间和癫痫发作后的结局。实验结束后采集样本,进行转录组测序分析。OE生物技术有限公司(上海,中国)负责样品Methylation EPIC Bead Chip实验结果和数据分析的进行。结果:转录组相关测序显示癫痫发作改变小鼠脑组织海马区小胶质细胞M2型的基因表达,其中表达上调基因245个,表达下调基因88个,GO富集分析显示上调基因富集于影响小胶质细胞生长和增殖的通路。结论:癫痫发作改变小鼠海马区小胶质细胞的基因表达且富集于抑制小胶质细胞生长发育通路。Objective: To study the gene enrichment of microglia in hippocampal region of C57 mouse brain after polarization induced by epilepsy. Methods: 40 C57 mice were randomly divided into control group (12 in CNC group) and epilepsy group (28 in OPTZ group). The CNC group was intraperitoneally injected with normal saline every other day, and the OPTZ group was intraperitoneally injected with pentatetrazole every other day for 28 days. In the course of the experiment to induce epilepsy, the daily behavior of the mouse, the degree of seizure, the duration of seizure and the outcome after seizure were observed. After the experiment, the samples were collected and analyzed by transcriptome sequencing. OE Biotechnology Co. Ltd. (Shanghai, China) was responsible for the experimental results and data analysis of the sample, Methylation EPIC Bead Chip. Results: Transcriptome sequencing showed that seizures changed the M2 gene expression of microglia in the hippocampus of mouse brain tissue, including 245 up-regulated genes and 88 down-regulated genes. GO enrichment analysis showed that up-regulated genes were enriched in the pathway affecting the growth and proliferation of microglia. Conclusion: Epileptic seizure changes the gene expression of microglia in the hippocampus of mouse and is concentrated in the pathway that inhibits the growth and development of microglia.
基金Supported by the Zhejiang Provincial Natural Science Foundation of China(No.LR21D060003)the National Key Research and Development Program of China(No.2017YFA0604904)。
文摘Sebastiscus marmoratus is one of the ideal fish species for offshore breeding,and temperature changes directly affect its physiological process.We performed whole-transcriptome sequencing of the liver tissues of S.marmoratus under heat stress(25℃),normal condition(20℃,the control),and cold stress(15℃).A total of 376 differentially expressed genes(DEGs),147 differentially expressed lncRNAs(DELs),and 40 differentially expressed miRNAs(DEMis)were detected under heat stress;59 DEGs,59 DELs,and 44 DEMis were detected under cold stress.Furthermore,a competing endogenous RNA regulatory network for the functional interaction of lncRNA-miRNA-mRNA was constructed,and GO and KEGG enrichment analyses showed that genes involved in maintaining homeostasis or adjusting to stress and stimulation were strongly activated during heat stress.Including heat-shock protein-related genes Hsp70,FKBP4,and Hspa4a regulated by dre-mir-205-5p;energy metabolism-related genes GCK,g6pca,and RFK regulated by dre-miR-205-5p,dre-miR-145-5p,novel_441,TCONS_00023692,and tcon_00095578;and immune-related genes SCAF,NLRC3,per1b,herc4,MafG,and KLHL29 regulated by dre-miR-456,novel_640,novel_163,TCONS_00079377,TCONS_00063590,and TCONS_000605708.Our findings provide new insights into the adaptation of S.marmoratus to acute temperature changes.
