Gastric cancer(GC)is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide.There is an increasing understanding of the roles that genetic and epigenetic alterations...Gastric cancer(GC)is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide.There is an increasing understanding of the roles that genetic and epigenetic alterations play in GCs.Recent studies using nextgeneration sequencing(NGS)have revealed a number of potential cancer-driving genes in GC.Whole-exome sequencing of GC has identified recurrent somatic mutations in the chromatin remodeling gene ARID1A and alterations in the cell adhesion gene FAT4,a member of the cadherin gene family.Mutations in chromatin remodeling genes(ARID1A,MLL3 and MLL)have been found in 47%of GCs.Whole-genome sequencing and whole-transcriptome sequencing analyses have also discovered novel alterations in GC.Recent studies of cancer epigenetics have revealed widespread alterations in genes involved in the epigenetic machinery,such as DNA methylation,histone modifications,nucleosome positioning,noncoding RNAs and microRNAs.Recent advances in molecular research on GC have resulted in the introduction of new diagnostic and therapeutic strategies into clinical settings.The antihuman epidermal growth receptor 2(HER2)antibody trastuzumab has led to an era of personalized therapy in GC.In addition,ramucirumab,a monoclonal antibody targeting vascular endothelial growth factor receptor(VEGFR)-2,is the first biological treatment that showed survival benefits as a single-agent therapy in patients with advanced GC who progressed after firstline chemotherapy.Using NGS to systematically identify gene alterations in GC is a promising approach with remarkable potential for investigating the pathogenesis of GC and identifying novel therapeutic targets,as well as useful biomarkers.In this review,we will summarize the recent advances in the understanding of the molecular pathogenesis of GC,focusing on the potential use of these genetic and epigenetic alterations as diagnostic biomarkers and novel therapeutic targets.展开更多
MicroRNAs （miRNAs） are endogenous -22 nt RNAs that play important regulatory roles in targeting mRNAs for cleavage or translational repression. Despite the discovery of increasing numbers of human and mouse miRNAs, ...MicroRNAs （miRNAs） are endogenous -22 nt RNAs that play important regulatory roles in targeting mRNAs for cleavage or translational repression. Despite the discovery of increasing numbers of human and mouse miRNAs, little is known about miRNAs from pig. In this study, we sought to extend the repertoire of porcine small regulatory RNAs using Solexa sequencing. We sequenced a library of small RNAs prepared from immortalized swine umbilical vein endothelial cells （SUVECs）. We produced over 13.6 million short sequence reads, of which 8 547 658 perfectly mapped to the pig genome. A bioinformatics pipeline was used to identify authentic mature miRNA sequences. We identified 154 porcine miRNA genes, among which 146 were conserved across species, and 8 were pig-specific miRNA genes. The 146 miRNA genes encoded 116 conserved mature miRNAs and 66 miRNA^＊. The 8 pig-specific miRNA genes encoded 4 mature miRNAs. Four potential novel miRNAs were identified. The secondary structures of the 154 miRNA genes were predicted; 13 miRNAs have 2 structures, and miR-9 and miR-199 have 4 and 3 structures, respectively. 36 miRNAs were organized into 19 compact clusters, miR-206, miR-21 and miR-378 were the relatively highly expressed miRNAs. In conclusion, Solexa sequencing allowed the successful discovery of known and novel porcine miRNAs with high accuracy and efficiency. Furthermore, our results supply new data to the somewhat insufficient pig miRBase, and are useful for investigating features of the blood-brain barrier, vascular diseases and inflammation.展开更多
Micro RNAs(mi RNAs) have been shown to play critical regulatory roles in gene expression in cotton. Although a large number of mi RNAs have been identified in cotton fibers, the functions of mi RNAs in seed developmen...Micro RNAs(mi RNAs) have been shown to play critical regulatory roles in gene expression in cotton. Although a large number of mi RNAs have been identified in cotton fibers, the functions of mi RNAs in seed development remain unexplored. In this study, a small RNA library was constructed from cotton seeds sampled at 15 days post-anthesis(DPA) and was subjected to high-throughput sequencing. A total of 95 known mi RNAs were detected to be expressed in cotton seeds. The expression pattern of these identified mi RNAs was profiled and 48 known mi RNAs were differentially expressed between cotton seeds and fibers at 15 DPA. In addition, 23 novel mi RNA candidates were identified in 15-DPA seeds. Putative targets for 21 novel and 87 known mi RNAs were successfully predicted and 900 expressed sequence tag(EST) sequences were proposed to be candidate target genes, which are involved in various metabolic and biological processes, suggesting a complex regulatory network in developing cotton seeds. Furthermore, mi RNA-mediated cleavage of three important transcripts in vivo was validated by RLM-5′ RACE. This study is the first to show the regulatory network of mi RNAs that are involved in developing cotton seeds and provides a foundation for future studies on the specific functions of these mi RNAs in seed development.展开更多
为探究miRNA(microRNA)在向日葵种子油脂合成中的作用,解析植物油脂合成分子调控机制,基于前期高油酸向日葵种子三个发育时期(开花后7 d、22 d、37 d)miRNA测序的结果,对影响油脂合成代谢的miRNA进行挖掘和表达分析。结果发现L7d vs L22...为探究miRNA(microRNA)在向日葵种子油脂合成中的作用,解析植物油脂合成分子调控机制,基于前期高油酸向日葵种子三个发育时期(开花后7 d、22 d、37 d)miRNA测序的结果,对影响油脂合成代谢的miRNA进行挖掘和表达分析。结果发现L7d vs L22d、L7d vs L37d和L22d vs L37d三组比较中参与油脂代谢通路的差异表达miRNA共有22个。表达量聚类热图分析发现,22d vs 37d比较组中大部分miRNA下调表达,表明油脂代谢相关的大部分miRNA在开花后37 d相比于22 d表达量降低。将靶基因注释到脂肪酸和三酰甘油合成通路中的22个差异表达miRNA在种子发育不同时期的表达量与种子含油量和脂肪酸组分进行相关性分析,结果分别发现己酸与miR172a3,十三烷酸与miR171b2均呈极显著负相关,油分含量与miR167d5p呈显著正相关,表明这些miRNA可能参与油脂的合成。通过共表达分析发现,有6对油脂代谢相关的miRNA(miR166u、miR171b_2、miR397a_3、miR157d、miR167a-5p、miR169v_1)与其靶基因呈负相关的共表达关系,表明这些基因的差异表达可能是miRNA调控的结果。展开更多
MicroRNAs (miRNAs),a class of small non-coding RNAs,are crucial endogenous gene regulators in a range of animals,including plant-parasitic nematodes.Meloidogyne graminicola is an obligate sedentary endoparasite of ric...MicroRNAs (miRNAs),a class of small non-coding RNAs,are crucial endogenous gene regulators in a range of animals,including plant-parasitic nematodes.Meloidogyne graminicola is an obligate sedentary endoparasite of rice and causes significant yield losses.A number of studies focused on the roles of M.graminicola effectors during the parasitic process;however,how nematode miRNAs regulate its effectors needs elucidating.In this research,we analyzed a cluster of M.graminicola miRNAs obtained at the second-stage juveniles (J2s) stage that are closely linked to the regulation of M.graminicola effectors.There are 49 767 105 total clean reads obtained from three libraries.A total of 233 known miRNAs and 21 novel miRNAs were identified.Among the known miRNAs,mgr-lin-4,mgr-mir-1,mgr-mir-100,mgrmir-86,mgr-mir-279,mgr-mir-87,mgr-mir-71,mgr-mir-9,mgr-mir-50,mgr-mir-72,and mgr-mir-34 are the most abundant11 miRNAs families.Moreover,the expression levels of selected miRNAs were validated by real-time quantitative PCR.We hypothesized that these miRNAs might regulate the expression of secreted effectors during the J2s stage to facilitate its infection.Consistent with this,we found that mgr-mir-9 targets MgPDI,an important M.graminicola effector mRNA.In addition to that,J2s treated with mgr-mir-9 mimics showed down-regulation of MgPDI expression and reduced reproductive ability,alluding mgr-mir-9 is involved in nematode infection.These results provide novel insight into the regulatory functions of M.graminicola miRNAs during the infection and identify miRNAs and their effector targets as potential key management targets to limit parasite survival during the early stages of infection.展开更多
基金Supported by Grants-in-Aid for Scientific Research from the Ministry of Education,Culture,Sports,Science and Technology of Japan
文摘Gastric cancer(GC)is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide.There is an increasing understanding of the roles that genetic and epigenetic alterations play in GCs.Recent studies using nextgeneration sequencing(NGS)have revealed a number of potential cancer-driving genes in GC.Whole-exome sequencing of GC has identified recurrent somatic mutations in the chromatin remodeling gene ARID1A and alterations in the cell adhesion gene FAT4,a member of the cadherin gene family.Mutations in chromatin remodeling genes(ARID1A,MLL3 and MLL)have been found in 47%of GCs.Whole-genome sequencing and whole-transcriptome sequencing analyses have also discovered novel alterations in GC.Recent studies of cancer epigenetics have revealed widespread alterations in genes involved in the epigenetic machinery,such as DNA methylation,histone modifications,nucleosome positioning,noncoding RNAs and microRNAs.Recent advances in molecular research on GC have resulted in the introduction of new diagnostic and therapeutic strategies into clinical settings.The antihuman epidermal growth receptor 2(HER2)antibody trastuzumab has led to an era of personalized therapy in GC.In addition,ramucirumab,a monoclonal antibody targeting vascular endothelial growth factor receptor(VEGFR)-2,is the first biological treatment that showed survival benefits as a single-agent therapy in patients with advanced GC who progressed after firstline chemotherapy.Using NGS to systematically identify gene alterations in GC is a promising approach with remarkable potential for investigating the pathogenesis of GC and identifying novel therapeutic targets,as well as useful biomarkers.In this review,we will summarize the recent advances in the understanding of the molecular pathogenesis of GC,focusing on the potential use of these genetic and epigenetic alterations as diagnostic biomarkers and novel therapeutic targets.
基金supported by grants from the National Natural Science Foundation of China (30771607)
文摘MicroRNAs （miRNAs） are endogenous -22 nt RNAs that play important regulatory roles in targeting mRNAs for cleavage or translational repression. Despite the discovery of increasing numbers of human and mouse miRNAs, little is known about miRNAs from pig. In this study, we sought to extend the repertoire of porcine small regulatory RNAs using Solexa sequencing. We sequenced a library of small RNAs prepared from immortalized swine umbilical vein endothelial cells （SUVECs）. We produced over 13.6 million short sequence reads, of which 8 547 658 perfectly mapped to the pig genome. A bioinformatics pipeline was used to identify authentic mature miRNA sequences. We identified 154 porcine miRNA genes, among which 146 were conserved across species, and 8 were pig-specific miRNA genes. The 146 miRNA genes encoded 116 conserved mature miRNAs and 66 miRNA^＊. The 8 pig-specific miRNA genes encoded 4 mature miRNAs. Four potential novel miRNAs were identified. The secondary structures of the 154 miRNA genes were predicted; 13 miRNAs have 2 structures, and miR-9 and miR-199 have 4 and 3 structures, respectively. 36 miRNAs were organized into 19 compact clusters, miR-206, miR-21 and miR-378 were the relatively highly expressed miRNAs. In conclusion, Solexa sequencing allowed the successful discovery of known and novel porcine miRNAs with high accuracy and efficiency. Furthermore, our results supply new data to the somewhat insufficient pig miRBase, and are useful for investigating features of the blood-brain barrier, vascular diseases and inflammation.
基金supported by the National Basic Research Program of China(2010CB126003)the National Transgenic Animals and Plants Research Project(2011ZX08005-003,2011ZX08009-003)
文摘Micro RNAs(mi RNAs) have been shown to play critical regulatory roles in gene expression in cotton. Although a large number of mi RNAs have been identified in cotton fibers, the functions of mi RNAs in seed development remain unexplored. In this study, a small RNA library was constructed from cotton seeds sampled at 15 days post-anthesis(DPA) and was subjected to high-throughput sequencing. A total of 95 known mi RNAs were detected to be expressed in cotton seeds. The expression pattern of these identified mi RNAs was profiled and 48 known mi RNAs were differentially expressed between cotton seeds and fibers at 15 DPA. In addition, 23 novel mi RNA candidates were identified in 15-DPA seeds. Putative targets for 21 novel and 87 known mi RNAs were successfully predicted and 900 expressed sequence tag(EST) sequences were proposed to be candidate target genes, which are involved in various metabolic and biological processes, suggesting a complex regulatory network in developing cotton seeds. Furthermore, mi RNA-mediated cleavage of three important transcripts in vivo was validated by RLM-5′ RACE. This study is the first to show the regulatory network of mi RNAs that are involved in developing cotton seeds and provides a foundation for future studies on the specific functions of these mi RNAs in seed development.
文摘为探究miRNA(microRNA)在向日葵种子油脂合成中的作用,解析植物油脂合成分子调控机制,基于前期高油酸向日葵种子三个发育时期(开花后7 d、22 d、37 d)miRNA测序的结果,对影响油脂合成代谢的miRNA进行挖掘和表达分析。结果发现L7d vs L22d、L7d vs L37d和L22d vs L37d三组比较中参与油脂代谢通路的差异表达miRNA共有22个。表达量聚类热图分析发现,22d vs 37d比较组中大部分miRNA下调表达,表明油脂代谢相关的大部分miRNA在开花后37 d相比于22 d表达量降低。将靶基因注释到脂肪酸和三酰甘油合成通路中的22个差异表达miRNA在种子发育不同时期的表达量与种子含油量和脂肪酸组分进行相关性分析,结果分别发现己酸与miR172a3,十三烷酸与miR171b2均呈极显著负相关,油分含量与miR167d5p呈显著正相关,表明这些miRNA可能参与油脂的合成。通过共表达分析发现,有6对油脂代谢相关的miRNA(miR166u、miR171b_2、miR397a_3、miR157d、miR167a-5p、miR169v_1)与其靶基因呈负相关的共表达关系,表明这些基因的差异表达可能是miRNA调控的结果。
基金financially supported by the National Natural Science Foundation of China (32001877)。
文摘MicroRNAs (miRNAs),a class of small non-coding RNAs,are crucial endogenous gene regulators in a range of animals,including plant-parasitic nematodes.Meloidogyne graminicola is an obligate sedentary endoparasite of rice and causes significant yield losses.A number of studies focused on the roles of M.graminicola effectors during the parasitic process;however,how nematode miRNAs regulate its effectors needs elucidating.In this research,we analyzed a cluster of M.graminicola miRNAs obtained at the second-stage juveniles (J2s) stage that are closely linked to the regulation of M.graminicola effectors.There are 49 767 105 total clean reads obtained from three libraries.A total of 233 known miRNAs and 21 novel miRNAs were identified.Among the known miRNAs,mgr-lin-4,mgr-mir-1,mgr-mir-100,mgrmir-86,mgr-mir-279,mgr-mir-87,mgr-mir-71,mgr-mir-9,mgr-mir-50,mgr-mir-72,and mgr-mir-34 are the most abundant11 miRNAs families.Moreover,the expression levels of selected miRNAs were validated by real-time quantitative PCR.We hypothesized that these miRNAs might regulate the expression of secreted effectors during the J2s stage to facilitate its infection.Consistent with this,we found that mgr-mir-9 targets MgPDI,an important M.graminicola effector mRNA.In addition to that,J2s treated with mgr-mir-9 mimics showed down-regulation of MgPDI expression and reduced reproductive ability,alluding mgr-mir-9 is involved in nematode infection.These results provide novel insight into the regulatory functions of M.graminicola miRNAs during the infection and identify miRNAs and their effector targets as potential key management targets to limit parasite survival during the early stages of infection.
