Identification of tRFs&tiRNAs Expression Profile in Breast Cancer Tissues
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ABSTRACT:
PROVIDER: PRJNA510401 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8330380.fastq.gz | Fastqsanger.gz | |||
| SRR8330381.fastq.gz | Fastqsanger.gz | |||
| SRR8330382.fastq.gz | Fastqsanger.gz | |||
| SRR8330383.fastq.gz | Fastqsanger.gz | |||
| SRR8330374.fastq.gz | Fastqsanger.gz |
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Project description:Purpose:In recent years, tRFs(transfer RNA-Derived Fragments) & tiRNAs (transfer RNA-Derived Stress-induced RNAs or tRNA halves) have been shown to have vital roles in cancer biology. We aimed to reveal the expression profile of tRFs&tiRNAs in breast cancer tissues in the study, and to explore their potential as biomarkers of breast cancer. Methods:We characterize tRFs&tiRNAs expression profiles in 6 pairs of breast cancer tissues and adjacent normal samples.Then we selected six tRFs&tiRNAs with significant expression and added 10 pairs of samples to verify the selected genes by qPCR in 16 pairs of breast cancer tissues along with the previous 6 pairs. Results:We found 31 differentially expressed tRFs&tiRNAs across our dataset, out of which 17 were up-regulated, 14 were down-regulated. Compared with 16 breast cancer tissues and healthy controls by qPCR, the results demonstrated that AS-tDR-001430, AS-tDR-001130 and AS-tDR-000779 were significantly expressed in breast cancer tissues (p < 0.001). AS-tDR-000779 was significantly up-regulated, AS-tDR-001430 and AS-tDR-001130 were significantly down-regulated which the expression patterns were similar to the sequencing results. Conclusions:Our studies have demonstrated that there were significantly expressed tRFs&tiRNAs in breast cancer tissues. They are hopefully to become biomarkers and would be valuable researches in this area.
2020-01-21 | GSE123967 | GEO
Project description:Purposes: To investigate the biological function of tRF in breast cancer by tRF and tiRNA sequencing Methods: Breast cancer tissue samples and matched non-tumor adjacent tissues were obtained from five patients. Small RNA sequencing was performed on Illumina NexSeq instrument Results: If P ≤ 0.05, fold change ≥ 2 as the cut off, there were 3 up-regulated tRFs & tiRNAs and 13 down-regulated tRFs & tiRNAs. Conclusions:There were 3 up-regulated tRFs & tiRNAs and 13 down-regulated tRFs & tiRNAs in breast cancer tissue samples and matching adjacent tissue samples
2022-01-01 | GSE192737 | GEO
Project description:Purpose: To explore the expression and biological functions of tRFs & tiRNAs in BALB/c mice with AD. Method: tRFs/tiRNAs profiles of control mice skin and 2,4-dinitrochlorobenzene(DNCB)- induced mice skin were generated by the Arraystar Mouse Small RNA Arrays. qRT–PCR validation was performed using SYBR Green assays. Results: There were 676 tRFs/tiRNAs that were aberrantly expressed in BALB/c mice with AD; 298 were upregulated and 378 were downregulated. tRF5-20-GluCTC-1, 5'tiRNA-33-ProTGG-4, 5'tRF-GluTTC, and mt-tRF3a-ProTGG were significantly expressed and confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the Small RNA microarray technology. Conclusion: The pathogenesis of AD may be related with the differential expression of tRFs/tiRNAs. These findings may provide new perspectives for elucidating the molecular mechanisms and future treatments for AD.
2023-05-31 | GSE225968 | GEO
Project description:tRFs&tiRNAs sequence in LUAD tissues with micropapillary /solid (High-Risk) component
| PRJNA1130887 | ENA
Project description:Despite being the leading cause of lung cancer death, the underlying molecular mechanisms driving metastasis progression are still not fully understood. tRNAs can generate a group of 18-40nt small RNA fragments named tRNA-derived small RNAs (tsRNAs) or tRNA-derived fragments (tRFs). Transfer RNA-derived fragments (tRFs) have been implicated in various biological processes in cancer. However, the role of tRFs in the development and progression of lung adenocarcinoma (LUAD) remains unclear. In the present study, we hypothesized that certain tRFs might become induced during LUAD metastatic progression. In this study, micropapillary and solid component was defined as high-risk, other component was defined as low-risk and adjcent tissue was defined as normal control. Our data revealed a series of dysregulated tRFs in 3 paired LUAD high-risk tissues, low-risk tissues and normal controls.
2024-07-04 | GSE271302 | GEO
Project description:Purpose: To study the expression and potential significance of tRF and tiRNA in PTC (Papillary thyroid carcinoma) by sequencing tRF and tiRNA in PTC tissues and corresponding paracancer tissues of thyroid cancer patients. Methods: Four pairs of PTC tissues and paracancer tissues were collected. Small RNA sequencing was performed on Illumina NexSeq instrument. Results: If P ≤ 0.05, fold change > 1.5 as the cutoff, there were 27 up-regulated tRFs & tiRNAs and 20 down-regulated tRFs & tiRNAs. Conclusions: Among the differentially expressed tRFs & tiRNAs, tiRNA-1:34-Lys-CTT-2 and tRF-1:30-Gly-CCC-3 may be the potential novel regulatory factors.
2022-02-26 | GSE197438 | GEO
Project description:Transfer RNA-derived fragments (tRFs) and transfer RNA halves (tiRNAs) have been shown to play crucial roles in gene regulation. This study targets to reveal the expression profile of tRFs and tiRNAs and their possible biological roles in lung adenocarcinoma (LUAD). Five paired clinical lung adenocarcinoma tissues (LAT) and adjacent normal lung tissues (ANLT) were selected to conduct the expression of tRFs and tiRNAs. The sequencing results showed that 109 tRFs and tiRNAs were differentially expressed between LAT and ANLT, out of which 60 were upregulated and 49 were downregulated. Compared with ANLT, lower expression levels of three tRF-1s (tRF-Ser-TGA-010, tRF-Arg-CCT-018 and tRF-Val-CAC-017) in LAT were verified by quantitative real-time polymerase chain reaction. Subsequently, the putative target genes of tRF-1s were analyzed by computational prediction and the top ten significant results of GO and KEGG pathway enrichment analysis were presented. These signaling pathways are involved in the carcinogenesis of LUAD. This study has showed a landscape of tRFs and tiRNAs expression profiles in LUAD. Three newly found differentially expressed down-regulated tRF-1s may be involved in the pathogenesis of LUAD and might serve as potential diagnostic biomarkers.
2022-01-19 | GSE165918 | GEO
Project description:tRFs/tiRNAs expression signature of low-glucose-treated HPAF-II cells
| PRJNA864823 | ENA
Project description:Purpose: to explore the function and mechanism of skin damage induced by ultraviolet irradiation. Method: Skin tRF & tiRNA profiles of mice normal skin and damage skin induced by Ultraviolet Irradiation (UV) were generated by deep sequencing, using Illumina NextSeq 500. qRT–PCR validation was performed using SYBR Green assays. Results:Sequencing was used to screen expression profiles and predict target genes. Compared with normal skin, a total of 31 differentially expressed tRFs and tiRNAs were screened. Among these, 10 tRFs and tiRNAs were shown to be significantly different in expression levels, where there were 4 up-regulated and 6 down-regulated target genes.Altered expression of 4 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to skin repair after damage induced by ultraviolet irradiation. Conclusion: tRF-Trp-TCA-001 and tRF-Gly-CCC-019 plays an important role in acute skin injury induced by UVB radiation by regulating the ras-related C3 botulinum toxin substrate 1 (Rac1) gene in the WNT signaling pathway. This study provides new insights into the mechanisms and therapeutic targets of UV-induced skin injury.
2021-08-06 | GSE162641 | GEO
Project description:Background: Congenital heart disease (CHD) is one of the most predominant birth defects that cause infant death worldwide. The timely and successful surgical treatment of CHD on newborns after delivery requires accurate detection and reliable diagnosis during pregnancy. However, there are no biomarkers that can serve as an early diagnostic factor for CHD patients. tRNA-derived fragments (tRFs) have been reported to play an important role in the occurrence and progression of numerous diseases, but their roles in CHD remains unknown. Methods: High-throughput sequencing was performed on the peripheral blood of pregnant women with abnormal fetal heart and normal fetal heart, and 728 differentially expressed tRFs/tiRNAs were identified, among which the top 18 tRFs/tiRNAs were selected as predictive biomarkers of CHD. Then, quantitative reverse transcriptase polymerase chain reaction verified the expression of tRFs/tiRNAs in more clinical samples, and the correlation between tRFs/tiRNAs abnormalities and CHD was analyzed. Results: tRF-58:74-Gly-GCC-1 and tiRNA-1:35-Leu-CAG-1-M2 may be promising biomarkers. Through further bioinformatics analysis, we predicted that TRF-58:744-GLy-GCC-1 could induce CHD by influencing biological metabolic processes. Conclusions: our results provide a theoretical basis for the abnormally expressed tRF-58:74-Gly-GCC-1 in maternal peripheral blood as a new potential biomarker for the accurate diagnosis of CHD during pregnancy.
2023-03-01 | GSE221349 | GEO