Differentially expressed tRFs in CD5 positive relapsed &amp; refractory diffuse large B cell lymphoma and the bioinformatic analysis for their potential clinical use

Qu, Qingyuan; Li, Ying; Fang, Xiaosheng; Zhang, Lingyan; Xue, Chao; Ge, Xueling; Wang, Xin; Jiang, Yujie

doi:10.1186/s13062-019-0255-8

Cited by 18 publications

(21 citation statements)

References 41 publications

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“…GO and KEGG analysis of the target genes of AS-tDR-013492 and AS-tDR-008946 proved that the target genes NEDD4L and UBA52 and several correlated pathways (PI3K/AKT and MAPK/ERK) may participate in the formation of CD5 + R/RDLBCL (26). The preliminary research on tRFs may supply a critical means for exploring the pathogenesis and progress of CD5 + R/R (relapsed & regenerative) DLBCL (26). Some scholars identi ed 8 differentially expressed tRFs by RNA-seq and qRT-PCR in good model of brain aging and related diseases (27).…”

Section: Discussionmentioning

confidence: 98%

“…The experimental consequence proved that tsRNAs may become a new molecular target for intracerebral hemorrhage (25). It's reported that the CD5+ diffuse large B-cell lymphoma (DLBCL) tissues were found to have three differentially expressed tRFs (AS-tDR-013492, AS-tDR-011395, and AS-tDR-008946), as detected by RNA-seq and qRT-PCR (26). GO and KEGG analysis of the target genes of AS-tDR-013492 and AS-tDR-008946 proved that the target genes NEDD4L and UBA52 and several correlated pathways (PI3K/AKT and MAPK/ERK) may participate in the formation of CD5 + R/RDLBCL (26).…”

Section: Discussionmentioning

confidence: 99%

“…It's reported that the CD5+ diffuse large B-cell lymphoma (DLBCL) tissues were found to have three differentially expressed tRFs (AS-tDR-013492, AS-tDR-011395, and AS-tDR-008946), as detected by RNA-seq and qRT-PCR (26). GO and KEGG analysis of the target genes of AS-tDR-013492 and AS-tDR-008946 proved that the target genes NEDD4L and UBA52 and several correlated pathways (PI3K/AKT and MAPK/ERK) may participate in the formation of CD5 + R/RDLBCL (26). The preliminary research on tRFs may supply a critical means for exploring the pathogenesis and progress of CD5 + R/R (relapsed & regenerative) DLBCL (26).…”

Section: Discussionmentioning

confidence: 99%

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RNA-sequencing reveals the expression profiles of tsRNAs and their potential carcinogenic role in cholangiocarcinoma

Yan

Wang

et al. 2020

Preprint

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Background: Recently, the incidence of cholangiocarcinoma (CCA) has gradually increased. As CCA has a poor prognosis, the ideal survival rate is scarce for patients. The abnormal expressed tsRNA may regulate the progression of a variety of tumors, and tsRNA is expected to become a new diagnostic marker of cancer. However, the expression of tsRNA is obscure and should be elucidated in CCA.Methods: We collected CCA tissues and adjacent normal tissues from three patients. High-throughput RNA-seq was utilized to determine the overall expression profiles of tsRNA in CCA and adjacent normal tissues and to screen the tsRNAs that were differentially expressed. The biological effects and potential signaling pathways of dysregulated tsRNAs between the CCA and adjacent normal tissues were explored by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.Results: High-throughput RNA-seq totally demonstrated 535 dysregulated tsRNAs, of which 241 tsRNAs were upregulated and 294 tsRNAs were downregulated in CCA compared with adjacent normal tissues (|log2 (fold change)| >=1 and p value< 0.05). GO and KEGG enrichment analyses indicated that the target genes of dysregulated tRFs (tRF-34-JJ6RRNLIK898HR, tRF-38-0668K87SERM492V, tRF-39-0668K87SERM492E2) were mainly enriched in the Notch signaling pathway, Hippo signaling pathway, and cAMP signaling pathway and in growth hormone synthesis, secretion and action.Conclusion: Differentially expressed tRFs in CCA are enriched in many pathways associated with neoplasms, which may impact the progression of CCA.

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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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RNA-sequencing reveals the expression profiles of tsRNAs and their potential carcinogenic role in cholangiocarcinoma

Yan

Wang

et al. 2020

Preprint

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“…94 Qu et al used an Illumina NextSeq instrument to detect tRFs in CD5-positive cells of relapsed and refractory diffuse large B-cell lymphoma. 95 Methods for studying the roles of tRFs and tiRNAs Microarray and RNA-seq are effective tools for the highthroughput detection of tRF and tiRNA expression. Balatti et al performed a microarray analysis of tsRNA expression profiles of CLL and lung cancer, and found that tsRNA might be an important effector in the pathogenesis of cancer-related development.…”

Section: Methods For Studying Trfs and Tirnasmentioning

confidence: 99%

Action mechanisms and research methods of tRNA-derived small RNAs

Xie

Yao

et al. 2020

Sig Transduct Target Ther

173

146

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tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or precursor tRNAs. tRFs and tiRNAs play biological roles through a variety of mechanisms by interacting with proteins or mRNA, inhibiting translation, and regulating gene expression, the cell cycle, and chromatin and epigenetic modifications. The establishment and application of research technologies are important in understanding the biological roles of tRFs and tiRNAs. To study the molecular mechanisms of tRFs and tiRNAs, researchers have used a variety of bioinformatics and molecular biology methods, such as microarray analysis, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR); Northern blotting; RNA sequencing (RNA-seq); cross-linking, ligation and sequencing of hybrids (CLASH); and photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP). This paper summarizes the classification, action mechanisms, and roles of tRFs and tiRNAs in human diseases and the related signal transduction pathways, targeted therapies, databases, and research methods associated with them.

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“…Accurate and rapid diagnostic tests will be critical for achieving control of COVID-19. OMICs approaches and data integration have facilitated identi cation of biomarkers for many diseases [31][32][33][34][35] . Similarly, production models have been proven as useful tools 36,37 , however serology represents a critical step in the COVID-19 control.…”

Section: Introductionmentioning

confidence: 99%

Serological Determinants of COVID-19

Noce

Santoro

Marrone

et al. 2020

Preprint

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Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection spreaded rapidly worldwide, as far as it has become a global pandemic. Therefore, the introduction of serological tests useful for the determination of IgM and IgG antibodies, it has become the main diagnostic tool, useful for tracking the spread of the virus and consequently its containment. In our study we compared point of care test (POCT) lateral flow immunoassay (FIA) vs automated chemiluminescent immunoassay (CLIA), in order to assess their specificity and sensibility against COVID-19 antibodies detection. Results: We find that different specificities and sensitivities for IgG and IgM tests. Notably IgM POCT FIA method vs CLIA method (gold standard) has a low sensitivity (0.526), while POCT FIA method vs CLIA method (gold standard) test has a much higher sensitivity (0.937); further, with respect of IgG, FIA and CLIA could arguably provide the same information. Conclusions: FIA method could be helpful in assessing in short time, the possible contagiousness of subjects that for work reasons cannot guarantee “social distancing”.

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Differentially expressed tRFs in CD5 positive relapsed & refractory diffuse large B cell lymphoma and the bioinformatic analysis for their potential clinical use

Cited by 18 publications

References 41 publications

RNA-sequencing reveals the expression profiles of tsRNAs and their potential carcinogenic role in cholangiocarcinoma

RNA-sequencing reveals the expression profiles of tsRNAs and their potential carcinogenic role in cholangiocarcinoma

Action mechanisms and research methods of tRNA-derived small RNAs

Serological Determinants of COVID-19

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