Circulating small RNA profiling of patients with alveolar and cystic echinococcosis
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ABSTRACT:
PROVIDER: PRJNA970814 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24487923.fastq.gz | Fastqsanger.gz | |||
| SRR24487924.fastq.gz | Fastqsanger.gz | |||
| SRR24487925.fastq.gz | Fastqsanger.gz | |||
| SRR24487926.fastq.gz | Fastqsanger.gz | |||
| SRR24487927.fastq.gz | Fastqsanger.gz |
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Project description:Alveolar (AE) and cystic (CE) echinococcosis are two parasitic diseases caused by the tapeworms Echinococcus multilocularis and E. granulosus sensu lato (s. l.), respectively. Currently, AE and CE are mainly diagnosed by means of imaging techniques, supported by serology and clinical and epidemiological data. However, no viability markers that indicate parasite state during infection are available. Extracellular small RNAs (sRNAs) are short non-coding RNAs that can be secreted by cells through association with extracellular vesicles, proteins, or lipoproteins. Circulating sRNAs can show altered expression in pathological states; hence, they are intensively studied as biomarkers of several diseases. Here, we profiled the sRNA transcriptomes in the context of AE and CE to identify novel biomarkers to aid in medical decisions. For this, endogenous and parasitic sRNAs were analysed by sRNA sequencing in sera from disease negative, positive, and treated patients and patients harbouring a non-parasitic lesion. Consequently, 20 differentially expressed sRNAs associated with AE, CE and/or non-parasitic liver lesion were identified. Our results represent an in-depth characterisation of the effect E. multilocularis and E. granulosus s.l. exert on the extracellular sRNA landscape in human infections and provide a set of novel candidate biomarkers for both AE and CE detection.
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Project description:Hepatic echinococcosis (HE) caused by Echinococcus spp. transmitted from carnivores is known as a severe zoonotic disease that formed into hepatic cystic echinococcosis (HCE) and hepatic alveolar echinococcosis (HAE). It continues to be a serious public health issue around the world. HAE is uncommon infection which is characterized by poor prognosis but it is the most life-threatening compare to HCE. Many cases of HAE are recognized at forward stages because clinical symptoms may remain silent in about 10 years of incubation period. Several pathological cases could be observed including septicemia, abscess, recurrent cholangitis, and portal hypertensive gastrointestinal bleeding in untreated people. It is provided that correlated factors includes CD44, Soluble ST2 (sST2), Plasma IL-23, IL-27, and IL-5 for metastasis and prognosis for patients with HAE were identified. However, data on metastatic and prognostic marker are still so poor. Recent studies have revealed that circRNAs are enriched and stable in exosomes. Exosomal circRNAs may be localized in platelet-derived extracellular vesicles, hepatic cells, and pancreatic cancer cells. Studies have suggested that it is possible that cells may transfer circRNAs by excreting them in exosomes. Whereas there are a lot of studies on cancer and other human diseases related exosomal circRNA, no studies on hepatic alveolar echinococcosis-related exosomal circRNAs in humans. Current study provides that exosomal circular RNAs from healthy humans and humans with hepatic alveolar echinococcal disease were detected and characterized using the RNA sequencing.
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Project description:Alveolar (AE) and cystic (CE) echinococcosis are two parasitic diseases caused by the tapeworms Echinococcus multilocularis and E. granulosus sensu lato (s. l.), respectively. Currently, AE and CE are mainly diagnosed by means of imaging techniques, serology, and clinical and epidemiological data. However, no viability markers that indicate parasite state during infection are available. Extracellular small RNAs (sRNAs) are short non-coding RNAs that can be secreted by cells through association with extracellular vesicles, proteins, or lipoproteins. Circulating sRNAs can show altered expression in pathological states; hence, they are intensively studied as biomarkers for several diseases. Here, we profiled the sRNA transcriptomes of AE and CE patients to identify novel biomarkers to aid in medical decisions when current diagnostic procedures are inconclusive. For this, endogenous and parasitic sRNAs were analyzed by sRNA sequencing in serum from disease negative, positive, and treated patients and patients harboring a non-parasitic lesion. Consequently, 20 differentially expressed sRNAs associated with AE, CE, and/or non-parasitic lesion were identified. Our results represent an in-depth characterization of the effect E. multilocularis and E. granulosus s. l. exert on the extracellular sRNA landscape in human infections and provide a set of novel candidate biomarkers for both AE and CE detection.
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Project description:Circulating RNAs are a less invasive and easy accessed source of samples for biomedical research and clinical applications. However, circulating mRNA is mostly fragmented and less abundant. High throughput RNA sequencing (RSEQ) and DASL assay have been both applied to profile such fragmented RNA samples. In this study, we compared the ability of transcriptomic profiling of the two platforms. Circulating RNAs from three non-small cell lung cancer patients and three age-matched healthy controls were analyzed by RSEQ and DASL assay. The concordance of each gene analyzed by the two platforms were measured with Pearson's correlation coefficient. And gene expression level determined by both platforms were confirmed by RT-PCR. The two platforms showed modest to moderate correlation. Genes with higher expression level represented higher cross-platform concordance. Compare the results of RT-PCR and the two platforms, RSEQ was much higher correlated with RT-PCR. This data suggested that RSEQ could be more suitable for circulating RNA profiling. In conclusion, we have demonstrated that genes with higher expression levels showed cross-platform concordance. And, the RSEQ could be more suitable tool for profiling circulating RNAs.
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Project description:Disparate Oxidant-related Gene Expression of Human Small Airway Epithelium Compared to Autologous Alveolar Macrophages in Response to the In Vivo Oxidant Stress of Cigarette Smoking The oxidant burden of cigarette smoking induces lung cell dysfunction, and play a significant role in the pathogenesis of lung disease. Two cell populations directly exposed to the oxidants in cigarette smoke are the small airway epithelium and alveolar macrophages. Of these, the epithelium appears to be more vulnerable to smoking, becoming disordered in differentiation, repair and function, while alveolar macrophages become activated, without becoming diseased. In this context, we asked: for the same individuals, what is the baseline trancriptome of oxidant-related genes in small airway epithelium compared to alveolar macrophages and do the responses of the transcriptome of these 2 cell populations differ substantially to inhaled cigarette smoke? To address these questions we used microarray gene expression and TaqMan analysis to assess the gene expression profile of known oxidant-related genes in paired samples recovered by bronchoscopy from small airway epithelium and alveolar macrophages from the same healthy nonsmokers and normal smokers. Of the 155 oxidant-related genes surveyed, 122 (77%) were expressed in both cell populations in nonsmokers. However, of the genes expressed by both cell populations, oxidant related gene expression levels were higher in alveolar macrophages (67 genes, 43%) than small airway epithelium (37 genes, 24%). There were more oxidant-related genes uniquely expressed in the small airway epithelium (17%), than in alveolar macrophages (5%). In healthy smokers, the majority of oxidant-related genes were expressed in both cell populations, but there were marked differences in the numbers of oxidant-related genes that smoking up- or down-regulated. While smoking up-regulated 15 genes (10%) and down-regulated 7 genes (5%) in the small airway epithelium, smoking had far less effect on alveolar macrophages [only 4 (3%) genes up-regulated, and only 1 (0.6%) down-regulated]. Only a small number of smoking responsive oxidant-related genes overlapped between the two cell types (2 up-regulated, and no down-regulated genes). Consistent with this observation, pathway analysis of smoking-responsive genes in the small airway epithelium showed oxidant-related pathways dominated, but in alveolar macrophages immune-response pathways dominated. Thus, the responses of the oxidant-related transcriptome of cells with an identical genome and exposed to the same oxidant stress of cigarette smoking are very different, with responses of oxidant-related genes of alveolar macrophages far more subdued than that of small airway epithelium, consistent with the clinical observation that, while the small airway epithelium is vulnerable, alveolar macrophages are not "diseased" in response to the oxidant stress of cigarette smoking. Gene expression profiles of known oxidant-related genes in paired samples recovered by bronchoscopy from small airway epithelium and alveolar macrophages from the same healthy nonsmokers and normal smokers.
2011-09-11 | E-GEOD-13931 | biostudies-arrayexpress