A Pilot Study for Protective Roles of tRNA-Derived Small RNA tRF-Ile-AAT-019 in Pathological Progression of Psoriasis
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PROVIDER: PRJNA702800 | ENA |
REPOSITORIES: ENA
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Project description:Psoriasis is a chronic recurrent inflammatory skin disease that is characterized by abnormal proliferation and differentiation of keratinocytes (KCs), angiogenesis and skin inflammation. tRNA-derived small RNA (tsRNA), including tRNA halves and tRNA fragments (tRFs), is a novel class of short non-coding RNA, possessing regulatory functions in many diseases. However, its role in the pathological development of psoriasis has been unknown. In this pilot study, we conducted small RNA sequencing to screen differentially expressed tRFs in psoriatic skin lesions as compared with normal controls. We found 130 upregulated and 104 downregulated tRFs, among which downregulation of tRF-Ile-AAT-019 in psoriatic skin lesions was further confirmed. Bioinformatics analysis by TargetScan and Miranda algorithms revealed that tRF-Ile-AAT-019 might target SERPINE1, thus regulating HIF-1α signaling pathway. We next showed that increased tRF-Ile-AAT-019 could downregulate expressions of SERPINE1, HIF-1α and vascular proliferative markers such as CD34, CD31, Factor VIII, and VEGF, but upregulate expressions of KCs differentiation markers including Keratin1 and Involucrin. Our data suggest that tRF-Ile-AAT-019 plays a protective role in the pathological progression of psoriasis via targeting SERPINE1 and blocking HIF-1α signaling pathway, leading to control KCs differentiation and vascular proliferation. This data provides a potential novel targeting pathway for the disease treatment.
2021-02-19 | GSE167057 | GEO
Project description:Corymbia citriodora strain:CV2-019 | cultivar:variegata CV2-019 Genome sequencing
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Project description:This project involves RNA-Seq analysis of samples obtained from the Phase IIA clinical trial TB-019 (NCT01669096) which evaluated kinetics of response, safety, and immunogenicity of the GSK Mycobacterium tuberculosis (MTB) vaccine M72/AS01E (“GSK M72”). GSK M72 consists of the M72 recombinant fusion of Mycobacterium tuberculosis (MTB) proteins Rv0125 and Rv1196 in combination with the liposome, TLR4 ligand (MPL), and QS21 saponin adjuvant AS01E (Leroux-Roels et al., 2013).
2023-12-30 | GSE102574 | GEO
Project description:tRNA fragments (tRFs) are small non-coding RNA molecules that are generated through the cleavage of tRNAs and have been implicated in various biological processes. Among the different types of tRFs, the 3′-tRFs have attracted considerable scientific interest due to their regulatory role in gene expression. In this study, we investigated the role of 3′-tRF-CysGCA, a tRF derived from cleavage in the T-loop of tRNACysGCA, in the regulation of gene expression in HEK-293 cells. Previous studies have shown that 3′-tRF-CysGCA is incorporated into the RISC complex and interacts with Argonaute proteins, suggesting its involvement in the regulation of gene expression. However, the general role and effect of the deregulation of 3′-tRF-CysGCA levels in human cells have not been investigated so far. To address this gap, we stably overexpressed 3′-tRF-CysGCA in HEK-293 cells and performed transcriptomics and proteomics experiments. Moreover, we validated the interaction of this tRF with putative targets whose levels were affected after 3′-tRF-CysGCA overexpression. Last, we investigated the implication of 3′-tRF-CysGCA in various pathways using extensive bioinformatics analysis. Our results indicate that 3′-tRF-CysGCA overexpression led to changes in the cell expression profile, and we identified multiple pathways that were affected by the deregulation of this tRF. Additionally, our reporter assays demonstrated that 3′-tRF-CysGCA directly interacted with TMPO and ERGIC1, leading to changes in their expression levels. Taken together, these findings suggest that 3′-tRF-CysGCA plays a significant role in the regulation of gene expression and highlight the potential importance of this tRF in cellular processes.
2023-11-30 | PXD044218 | Pride
Project description:Brucella suis 019 Genome sequencing and assembly
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Project description:Next generation sequencing was used to assess the changes along a diurnal cycle in the transcriptome of Drosophila head, periphery (entire body except the head) or the heart at 3, 5 or 7 weeks of age under ad libitum feeding (ALF) or time-restricted feeding (TRF). Next generation sequencing was used to assess the changes along a diurnal cycle in the transcriptome of Drosophila head, periphery (entire body except the head) or the heart at 3, 5 or 7 weeks of age under ad libitum feeding (ALF) or time-restricted feeding (TRF).
2015-02-18 | E-GEOD-64108 | biostudies-arrayexpress
Project description:Herein we demonstrate the efficacy of an unbiased proteomics screening approach for studying protein expression changes in the KC-Tie2 psoriasis mouse model, identifying multiple protein expression changes in the mouse and validating these changes in human psoriasis. KC-Tie2 mouse skin samples (n=3) were compared with littermate controls (n=3) using gel-based fractionation followed by label-free protein expression analysis. 5482 peptides mapping to 1281 proteins were identified and quantitated: 105 proteins exhibited fold-changes ≥2.0 including: stefin A1 (average fold change of 342.4 and an average P = 0.0082; cystatin A, human orthologue); slc25a5 (average fold change of 46.2 and an average P = 0.0318); serpinb3b (average fold change of 35.6 and an average P = 0.0345; serpinB1, human orthologue); and kallikrein related peptidase 6 (average fold change of 4.7 and an average P = 0.2474; KLK6). We independently confirmed mouse gene expression-based increases of selected genes including serpinb3b (17.4-fold, P < 0.0001), KLK6 (9.0-fold, P = 0.002), stefin A1 (7.3-fold; P < 0.001) and slc25A5 (1.5-fold; P = 0.05) using qRT-PCR on a second cohort of animals (n=8). Parallel LC/MS/MS analyses on these same samples verified protein-level increases of 1.3-fold (slc25a5; P < 0.05), 29,000-fold (stefinA1; P < 0.01), 322-fold (KLK6; P < 0.0001) between KC-Tie2 and control mice. To underscore the utility and translatability of our combined approach, we analyzed gene and protein expression levels in psoriasis patient skin and primary keratinocytes vs. healthy controls. Increases in gene expression for slc25a5 (1.8-fold), cystatin A (3.0-fold), KLK6 (5.8-fold) and serpinB1 (76-fold; all P < 0.05) were observed between healthy controls and involved lesional psoriasis skin and primary psoriasis keratinocytes. Moreover slc25a5, cystatin A, KLK6 and serpinB1 protein were all increased in lesional psoriasis skin compared to normal skin. These results highlight the usefulness of preclinical disease models using readily-available mouse skin and demonstrate the utility of proteomic approaches for identifying novel peptides/proteins that are differentially regulated in psoriasis that could serve as sources of auto-antigens or provide novel therapeutic targets for the development of new anti-psoriatic treatments.
2014-10-30 | PXD001387 | Pride
Project description:We first analyzed tsRNA signatures in SLE serum and identified that tRF-His-GTG-1 was significantly upregulated in SLE serum. The combination of tRF-His-GTG-1 and anti-dsDNA could serve as biomarkers for diagnosing SLE with a high AUC of 0.95 (95% CI=0.92-0.99), sensitivity (83.72%) and specificity (94.19%). Importantly, the non-invasive serum tRF-His-GTG-1 could also be used to distinguish SLE with LN or SLE without LN with AUC of 0.81 (95% CI, 0.73–0.88) and performance (sensitivity 66.27%, specificity 96.15%). Moreover, the serum tsRNA is mainly secreted via exosome and directly target signaling molecules that play crucial roles in regulating the immune system.
2021-11-09 | GSE179950 | GEO
Project description:The rapid development of high-throughput sequencing is conducive to the discovery of many new theories. The purpose of this study is to explore the differentially expressed of tRF & tiRNA in cholangiocarcinoma by high-throughput sequencing technology. We collected cholangiocarcinoma and adjacent normal tissues from three patients. After RNA extraction and RNA library preparation, we determined the raw data of tRF & tiRNA in cholangiocarcinoma and adjacent normal tissues by high-throughput RNA sequencing. Raw data were generated after sequencing,image analysis,basecalling and quality filtering on lllumina sequencer.Firstly,Q30 was used to perform quality control.The adaptor sequences were trimmed and the adaptor-trimmed-reads(>=16nt) were left by cut adapt software(v1.9.3).Then,the raw counts of each tRF&tiRNA(MINTbasev2.0) was calculated for all samples,defined as the raw expression level soft.The results showed that a total of 20102 tsRNA were detected in the two groups, 9616tsRNA were upregulated and 10486 were downregulated. There were 535 differentially expressed tsRNA in cholangiocarcinoma after edger standardization, of which 241 were upregulated and 294 were downregulated (| log2 (foldchange) | = 1andpvalue < 0.05). This study shows that high-throughput sequencing technology is helpful for us to determine the expression of tRF & tiRNA in cholangiocarcinoma, and to screen out differentially expressed tRF & tiRNA, and further to explore the factors that affect the progress of cholangiocarcinoma.
2021-10-31 | GSE147017 | GEO