Altered Expression Profiles of tRNA-derived fragments in relapsed/refractory multiple myeloma
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE171003 | GEO | 2021/05/19
REPOSITORIES: GEO
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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: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:We investigate tRF and tiRNA profiles in lung adenocarcinoma and adjacent tissues using a NextSeq system. Total RNA was extracted from tissues and pretreated to remove the RNA modifications. In patients with lung adenocarcinoma, 338 types of tRFs and tiRNAs were detected via sequencing, 284 of which were not previously reported. Compared with the adjacent tissues, 17 types of tRFs and tiRNAs comprising 34 subtypes were found to be abnormally expressed in lung adenocarcinoma tissues, 20 of which were upregulated and 14 of which were downregulated. Finally, we show that tRF and tiRNA profiles in lung adenocarcinoma and adjacent tissues and identify several dysregulated tRFs and tiRNAs.
2021-05-19 | GSE168270 | GEO
Project description:Purpose: to explore the function and mechanism of acute rejection in vascularized composite allotransplantation Method: tRF & tiRNA profiles of acute rejection in vascularized composite allotransplantation 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 the control group, there were significant differences in the expression levels of 16 tRFs & tiRNAs, including 5 up-regulated target genes and 11 down-regulated target genes. Bioinformatics analysis and RT-qPCR revealed potential up regulation of tRFs & tiRNAs(tiRNA-1-33-Gly-GCC-1, tiRNA-1-34-Glu-CTC-1, tRF-1-32-Gly-GCC-2-M2) and down regulation of tRFs & tiRNAs (tRF-59:75-Gln-CTG-2-M2, tRF-59:76-Val-AAC-1-M2). Conclusion: In conclusion, it is speculated that tiRNA-1-34-Glu-CTC-1 plays an important role in VCA induced acute rejection by regulating CACNA1D gene in MAPK signaling pathway. This provides a new insight into the mechanism and therapeutic targets of acute rejection.
2022-07-20 | GSE190008 | GEO
Project description:Purposes: To investigate the epigenetic mechanism of IBS-D(Irritable Bowel Syndrome with Diarrhea) by tRF & tiRNA sequencing in intestinal biopsies of IBS-D patients and healthy volunteers Methods: Five IBS-D and five healthy volunteers were screened, and biopsies were taken under colonoscopy. Small RNA sequencing was performed on Illumina NexSeq instrument Results:If P < 0.05, fold change > 1.5 as the cutoff, there were 14 up-regulated tRFs & tiRNAs and 14 down-regulated tRFs & tiRNAs. Conclusions:There were 14 up-regulated tRFs & tiRNAs and 14 down-regulated tRFs & tiRNAs in intestinal tissues of IBS-D .
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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: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
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: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:Background: As couples struggle with infertility and livestock producers wish to rapidly improve genetic merit in their herd, assisted reproductive technologies (ART) have become increasingly popular in human medicine as well as the livestock industry. Utilizing ART can cause an increased risk of congenital overgrowth syndromes, such as Large Offspring Syndrome (LOS) in ruminants. A dysregulation of transcripts has been observed in bovine fetuses with LOS, which is suggested to be a cause of the phenotype. Our recent study identified variations in tRNA expression in LOS individuals, leading us to hypothesize that variations in tRNA expression can influence the availability of their processed regulatory products, tRNA-derived fragments (tRFs). Due to their resemblance in size to microRNAs, studies suggest that tRFs target mRNA transcripts and regulate gene expression. Thus, we have sequenced small RNA isolated from skeletal muscle and liver of day 105 bovine fetuses to elucidate the mechanisms contributing to LOS. Moreover, we have utilized our previously generated tRNA sequencing data to analyze the contribution of tRNA availability to tRF abundance. Results: 22,289 and 7,737 unique tRFs were predicted in the liver and muscle tissue respectively. The greatest number of reads originated from 5′ tRFs in muscle and 5′ halves in liver. In addition, mitochondrial (MT) and nuclear derived tRF expression was tissue-specific with most MT-tRFs and nuclear tRFs derived from LysUUU and iMetCAU in muscle, and AsnGUU and GlyGCC in liver. Despite variation in tRF abundance within treatment groups, we identified differentially expressed (DE) tRFs across Control-AI, ART-Normal, and ART-LOS groups with the most DE tRFs between ART-Normal and ART-LOS groups. Many DE tRFs target transcripts enriched in pathways related to growth and development in the muscle and tumor development in the liver. Finally, we found positive correlation coefficients between tRNA availability and tRF expression in muscle (R = 0.47) and liver (0.6). Conclusion: Our results highlight the dysregulation of tRF expression and its regulatory roles in LOS. These tRFs were found to target both imprinted and non-imprinted genes in muscle as well as genes linked to tumor development in the liver. Furthermore, we found that tRNA transcription is a highly modulated event that plays a part in the biogenesis of tRFs. This study is the first to investigate the relationship between tRNA and tRF expression in combination with ART-induced LOS.
2022-11-15 | GSE213525 | GEO