The desmoplastic and complex tumor microenvironment of pancreatic ductal adenocarcinoma(PDAC)has presented tremendous challenges for developing effective therapeutic strategies.Strategies targeting tumor stroma,albeit...The desmoplastic and complex tumor microenvironment of pancreatic ductal adenocarcinoma(PDAC)has presented tremendous challenges for developing effective therapeutic strategies.Strategies targeting tumor stroma,albeit with great potential,have met with limited success due to the lack of knowledge on the molecular dynamics within the tumor microenvironment(TME).In pursuit of a better understanding of the influence of miRNAs on TME reprogramming and to explore circulating miRNAs as diagnostic and prognostic biomarkers for PDAC,using RNA-seq,miRNA-seq,and single-cell RNA-seq(scRNA-seq),we investigated the dysregulated signaling pathways in PDAC TME modulated by miRNAs from plasma and tumor tissue.Our bulk RNA-seq in PDAC tumor tissue identified 1445 significantly differentially expressed genes with extracellular matrix and structure organization as the top enriched pathways.Our miRNA-seq identified 322 and 49 abnormally expressed miRNAs in PDAC patient plasma and tumor tissue,respectively.We found many of the TME signaling pathways were targeted by those dysregulated miRNAs in PDAC plasma.Combined with scRNA-seq from patient PDAC tumor,our results revealed that these dysregulated miRNAs were closely associated with extracellular matrix(ECM)remodeling,cell-ECM communication,epithelial-mesenchymal transition,as well as immunosuppression orchestrated by different cellular components of TME.The findings of this study could assist the development of miRNA-based stromal targeting biomarkers or therapy for PDAC patients.展开更多
Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present st...Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and IncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during sternness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heine metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.展开更多
Background： MicroRNAs （miRNAs） regulate target gene expression at post-transcriptional level. Intense research has been conducted for miRNA identification and the target finding. However, much less is known about t...Background： MicroRNAs （miRNAs） regulate target gene expression at post-transcriptional level. Intense research has been conducted for miRNA identification and the target finding. However, much less is known about the transcriptional regulation of miRNA genes themselves. Recently, a special group of pre-miRNAs that are produced directly by transcription without Drosha processing were validated in mouse, indicating the complexity of miRNA biogenesis. Methods： In this work, we detect clusters of aligned Cap-seq reads to find the transcription start sites （TSSs） for intergenic miRNAs and study their transcriptional regulation in Caenorhabditis elegans and mouse. Results： In both species, we have identified a class of special pre-miRNAs whose 5＇ ends are capped, and are most probably generated directly by transcription. Furthermore, we distinguished another class of special pre-miRNAs that are 5＇-capped but are also part of longer primary miRNAs, suggesting they may have more than one transcription mechanism. We detected multiple cap reads peaks within miRNA clusters in C. elegans. We surmised that the miRNAs in a cluster may either be transcribed independently or be re-capped during the microprocessor cleavage process. We also observed that H3K4me3 and Pol II are enriched at those identified miRNA TSSs. Conclusions： The Cap-seq datasets enabled us to annotate the primary TSSs for miRNA genes with high resolution. Special class of 5＇-capped pre-miRNAs have been identified in both C. elegans and mouse. The capping patter of miRNAs in a cluster indicate that clustered miRNA transcripts probably undergo a re-capping procedure during the microprocessor cleavage process.展开更多
基金funded in part by the National Institutes of Health(Grant No.S10OD019960)(CW)the American Heart Association(Grant No.18IPA34170301)(CW)+1 种基金the Ardmore Institute of Health(Grant No.2150141)(CW)the partial support of the Loma Linda University School of Medicine GCAT Grant(CW).
文摘The desmoplastic and complex tumor microenvironment of pancreatic ductal adenocarcinoma(PDAC)has presented tremendous challenges for developing effective therapeutic strategies.Strategies targeting tumor stroma,albeit with great potential,have met with limited success due to the lack of knowledge on the molecular dynamics within the tumor microenvironment(TME).In pursuit of a better understanding of the influence of miRNAs on TME reprogramming and to explore circulating miRNAs as diagnostic and prognostic biomarkers for PDAC,using RNA-seq,miRNA-seq,and single-cell RNA-seq(scRNA-seq),we investigated the dysregulated signaling pathways in PDAC TME modulated by miRNAs from plasma and tumor tissue.Our bulk RNA-seq in PDAC tumor tissue identified 1445 significantly differentially expressed genes with extracellular matrix and structure organization as the top enriched pathways.Our miRNA-seq identified 322 and 49 abnormally expressed miRNAs in PDAC patient plasma and tumor tissue,respectively.We found many of the TME signaling pathways were targeted by those dysregulated miRNAs in PDAC plasma.Combined with scRNA-seq from patient PDAC tumor,our results revealed that these dysregulated miRNAs were closely associated with extracellular matrix(ECM)remodeling,cell-ECM communication,epithelial-mesenchymal transition,as well as immunosuppression orchestrated by different cellular components of TME.The findings of this study could assist the development of miRNA-based stromal targeting biomarkers or therapy for PDAC patients.
文摘Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and IncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during sternness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heine metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.
文摘Background： MicroRNAs （miRNAs） regulate target gene expression at post-transcriptional level. Intense research has been conducted for miRNA identification and the target finding. However, much less is known about the transcriptional regulation of miRNA genes themselves. Recently, a special group of pre-miRNAs that are produced directly by transcription without Drosha processing were validated in mouse, indicating the complexity of miRNA biogenesis. Methods： In this work, we detect clusters of aligned Cap-seq reads to find the transcription start sites （TSSs） for intergenic miRNAs and study their transcriptional regulation in Caenorhabditis elegans and mouse. Results： In both species, we have identified a class of special pre-miRNAs whose 5＇ ends are capped, and are most probably generated directly by transcription. Furthermore, we distinguished another class of special pre-miRNAs that are 5＇-capped but are also part of longer primary miRNAs, suggesting they may have more than one transcription mechanism. We detected multiple cap reads peaks within miRNA clusters in C. elegans. We surmised that the miRNAs in a cluster may either be transcribed independently or be re-capped during the microprocessor cleavage process. We also observed that H3K4me3 and Pol II are enriched at those identified miRNA TSSs. Conclusions： The Cap-seq datasets enabled us to annotate the primary TSSs for miRNA genes with high resolution. Special class of 5＇-capped pre-miRNAs have been identified in both C. elegans and mouse. The capping patter of miRNAs in a cluster indicate that clustered miRNA transcripts probably undergo a re-capping procedure during the microprocessor cleavage process.
