Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1109826 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28980178_1.fastq.gz | Fastqsanger.gz | |||
| SRR28980178_2.fastq.gz | Fastqsanger.gz | |||
| SRR28980179_1.fastq.gz | Fastqsanger.gz | |||
| SRR28980179_2.fastq.gz | Fastqsanger.gz | |||
| SRR28980180_1.fastq.gz | Fastqsanger.gz |
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Project description:To screen the differentially expressed lncRNAs, we performed lncRNA profiling using ArrayStar Human LncRNA Microarray in 24 new-onset systemic lupus erythematosus (SLE) patients and 12 age- and sex-matched healthy controls (HCs). For the lncRNA microarray screening, total RNA from plasma was isolated from 12 SLE without nephritis, 12 lupus nephritis (LN) and 12 HCs. Four RNA samples were mixed togther as a pool of sample for microarray analysis. Accordingly, there were each three pooled RNA samples from 12 SLE without nephritis, 12 LN and 12 HCs for microarray analysis. Hierarchical clustering showed the plasma levels of lncRNAs and mRNAs differed significantly between 24 new-onset SLE patients and 12 control subjects. With a fold change ≥ 2 and P ≤ 0.05, we identified 1315 significantly differentially expressed lncRNAs (743 lncRNAs up-regulated and 572 lncRNAs down-regulated) and 1363 differentially expressed mRNAs (745 mRNAs up-regulated and 618 mRNAs down-regulated) in plasma of SLE patients compared with control samples.
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Project description:long non-coding RNAs (lncRNAs) are novel non-coding RNAs which play an important part in regulating gene transcription and translation, modulating protein function, and acting as competing endogeneous RNA. Moveover, there is increasing evidence showing that aberrant expressions of lncRNAs are implicated in various cancers. Yet, their roles in systemic lupus erythematosus (SLE), a prototypical autoimmune disease, remain unknown. To reveal the implications of LncRNAs in SLE, we used Human LncRNA Array v3.0 microarrays to measure the expression profiles of lncRNAs in T cells of patients with SLE and healthy controls. we found 869 upregulated lncRNAs and 1066 downregulated lncRNAs in SLE patients compared with controls. Coding-non-coding gene coexpression (CNC) network was constructed based on the correlation analysis between the differentially expressed lncRNA and mRNA. Downregulation of two lncRNAs, uc001ykl.1 and ENST00000448942 was established using Real-time quantitative PCR. These results showed abrrant expression profiles of lncRNAs in T cells of SLE patients and revealed their potential role in SLE.
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Project description:Circular RNAs (circRNAs) are a novel class of non-coding RNA and stably conserved in mammalian cells. Although circRNAs have been widely reported in some diseases and tissues, the expression of circRNAs in systemic lupus erythematosus (SLE) have yet to be explored. To reveal the implications of circRNAs in SLE, we used Human circRNA Array v2.0 microarrays to measure the expression profiles of circRNAs in plasma of patients with SLE and healthy controls. A total of 4763 circRNAs were detected in plasma of SLE sample, and 112 circRNAs were identified to be differentially expressed in plasma of SLE patients as compared to healthy controls (fold change >1.5 and P < 0.05), including 53 up-regulated circRNAs and 59 down-regulated circRNAs. Hsa_circRNA_407176, hsa_circRNA_406567 and hsa_circRNA_001308 were established using Real-time quantitative PCR. These results showed abrrant expression profiles of circRNAs in T cells of SLE patients and revealed their potential role in SLE.
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Project description:Introduction: microRNAs are promising candidate breast cancer biomarkers due to their cancer-specific expression profiles. However, efforts to develop circulating breast cancer biomarkers are challenged by the heterogeneity of microRNAs in the blood. To overcome this challenge, we aimed to develop a molecular profile of microRNAs specifically secreted from breast cancer cells. Our first step towards this direction relates to capturing and analyzing the contents of exosomes, which are small secretory vesicles that selectively encapsulate microRNAs indicative of their cell of origin. To our knowledge, circulating exosome microRNAs have not been well evaluated as biomarkers for breast cancer diagnosis or monitoring. Methods: Exosomes were collected from the conditioned media of human breast cancer cell lines, mouse plasma of patient-derived orthotopic xenograft models (PDX), and human plasma samples. Exosomes were verified by electron microscopy, nanoparticle tracking analysis, and western blot. Cellular and exosome microRNAs from breast cancer cell lines were profiled by next-generation small RNA sequencing. Plasma exosome microRNA expression was analyzed by qRT-PCR analysis. Results: Small RNA sequencing and qRT-PCR analysis showed that several microRNAs are selectively encapsulated or highly enriched in breast cancer exosomes. Importantly, the selectively enriched exosome microRNA, human miR-1246, was detected at significantly higher levels in exosomes isolated from PDX mouse plasma, indicating that tumor exosome microRNAs are released into the circulation and can serve as plasma biomarkers for breast cancer. This observation was extended to human plasma samples where miR-1246 and miR-21 were detected at significantly higher levels in the plasma exosomes of 16 breast cancer patients as compared to the plasma exosomes of healthy control subjects. Receiver Operating Characteristic (ROC) curve analysis indicated that the combination of plasma exosome miR-1246 and miR-21 levels is a better indicator of breast cancer than their individual levels. Conclusions: Our results demonstrate that certain microRNA species, such as miR-21 and miR-1246, are selectively enriched in human breast cancer exosomes and significantly elevated in the plasma of breast cancer patients. These findings indicate a potential new strategy to selectively analyze plasma breast cancer microRNAs indicative of the presence of breast cancer.
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Project description:Long non-coding RNAs (lncRNAs) are pervasively expressed and have been reported as potential biomarkers and therapeutic targets in various diseases, including systemic lupus erythematosus (SLE). However, there was limited information about lncRNAs expression in kidney tissue with lupus nephritis (LN), a serious complication of SLE. To explore the underlying molecular and cellular mechanisms of lncRNAs during pathogenesis of LN, RNA sequencing (RNA_seq) was performed to determine the lncRNAs and mRNAs expression of kidney tissues from LN (MRL/lpr) and control mouse. We identified 12, 979 novel lncRNAs in mouse. The expression profiles of both mRNA and lncRNA were significant different between LN and control mouse. In particular, both upregulated lncRNAs and mRNAs were more than downregulated ones in kidney tissue of LN mouse. However, GO analysis showed that more downregulated genes were enriched in immune and inflammatory response associated pathway. KEGG analysis showed that both downregulated and upregulated genes were enriched in pathway including SLE pathway, about half of these SLE-assocaited genes were inflammatory factors. Moreover, we found that 2, 181 DElncRNAs potential targeted and regulated expresison of 778 mRNA in kidney tissues of LN. The results showed that 11 DE-LncRNAs targeted and co-expressed with six immune and SLE-assocaited genes. qPCR confirmed that lncRNA Gm20513 would positively regualte the expression of SLE-associated gene H2-Aa. In conclusion, our study demonstrates that lncRNA will influence the progression of LN and will provide some cues for further study of lncRNAs in LN. LncRNA-mRNA regulation network may have important value in LN diagnosis and therapy.
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