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】筛选出斑节对虾肌肉中与虾青素积累相关的基因及其信号通路,为揭示虾青素在对虾肌肉积累的分子机制提供基础数据。【方法】分别剪取注射虾青素斑节对虾(试验组)和未注射虾青素斑节对虾(对照组)的肌肉,提取RNA后等量混合构建cDN...【目的】筛选出斑节对虾肌肉中与虾青素积累相关的基因及其信号通路,为揭示虾青素在对虾肌肉积累的分子机制提供基础数据。【方法】分别剪取注射虾青素斑节对虾(试验组)和未注射虾青素斑节对虾(对照组)的肌肉,提取RNA后等量混合构建cDNA文库,采用Illumina HiSeq X Ten测序仪进行转录组测序,序列拼接与注释后以DESeq筛选差异表达基因(DEGs),然后进行GO功能注释分析和KEGG信号通路富集分析,并通过实时荧光定量PCR验证转录组数据的准确性。【结果】在试验组和对照组中分别获得48415832和48532230条有效序列(Clean reads),拼接后得到20495条Unigenes;分别有8761(占42.75%)、7658(占37.37%)、6933(占33.83%)、5584(占27.25%)和7238(占35.32%)条Unigenes在Nr、Swiss-Prot、KOG、KEGG和GO数据库中注释成功,其中在GO数据库的生物学过程、细胞组分、分子功能三大类别55个功能条目上均注释到Unigenes。经DESeq筛选,试验组与对照组间存在1468个DEGs,其中1209个DEGs在对照组呈上调表达、259个DEGs在对照组呈下调表达;与虾青素相关的基因主要有细胞色素b5基因(CYB5)、细胞色素P450基因(CYP450)、葡糖基/葡萄糖醛酸基转移酶基因(UDPGT)、类kelch蛋白基因(KLHL)、ATP结合盒转运蛋白基因(ABCT)、脂质蛋白受体基因(LipR)、脂肪酶基因(lipase)及半胱天冬酶3基因(CASP3)等。DEGs聚集最多的GO功能条目是多聚糖分解过程,富集最多的KEGG信号通路是信号转导。【结论】CYP450、CYB5、ABCT、LipR、KLHL、UDPGT、CASP3和lipase等DEGs,以及信号转导、运输与分解代谢、内分泌系统及辅酶因子和维生素代谢等信号通路与斑节对虾体内虾青素的积累相关,后续宜通过原位杂交、原核表达等技术验证DEGs的功能,进一步揭示虾青素在对虾体内积累的分子机制。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】筛选出斑节对虾肌肉中与虾青素积累相关的基因及其信号通路,为揭示虾青素在对虾肌肉积累的分子机制提供基础数据。【方法】分别剪取注射虾青素斑节对虾(试验组)和未注射虾青素斑节对虾(对照组)的肌肉,提取RNA后等量混合构建cDNA文库,采用Illumina HiSeq X Ten测序仪进行转录组测序,序列拼接与注释后以DESeq筛选差异表达基因(DEGs),然后进行GO功能注释分析和KEGG信号通路富集分析,并通过实时荧光定量PCR验证转录组数据的准确性。【结果】在试验组和对照组中分别获得48415832和48532230条有效序列(Clean reads),拼接后得到20495条Unigenes;分别有8761(占42.75%)、7658(占37.37%)、6933(占33.83%)、5584(占27.25%)和7238(占35.32%)条Unigenes在Nr、Swiss-Prot、KOG、KEGG和GO数据库中注释成功,其中在GO数据库的生物学过程、细胞组分、分子功能三大类别55个功能条目上均注释到Unigenes。经DESeq筛选,试验组与对照组间存在1468个DEGs,其中1209个DEGs在对照组呈上调表达、259个DEGs在对照组呈下调表达;与虾青素相关的基因主要有细胞色素b5基因(CYB5)、细胞色素P450基因(CYP450)、葡糖基/葡萄糖醛酸基转移酶基因(UDPGT)、类kelch蛋白基因(KLHL)、ATP结合盒转运蛋白基因(ABCT)、脂质蛋白受体基因(LipR)、脂肪酶基因(lipase)及半胱天冬酶3基因(CASP3)等。DEGs聚集最多的GO功能条目是多聚糖分解过程,富集最多的KEGG信号通路是信号转导。【结论】CYP450、CYB5、ABCT、LipR、KLHL、UDPGT、CASP3和lipase等DEGs,以及信号转导、运输与分解代谢、内分泌系统及辅酶因子和维生素代谢等信号通路与斑节对虾体内虾青素的积累相关,后续宜通过原位杂交、原核表达等技术验证DEGs的功能,进一步揭示虾青素在对虾体内积累的分子机制。
