YB1 regulates miR‐205/200b‐<i>ZEB1</i> axis by inhibiting microRNA maturation in hepatocellular carcinoma

Liu, Xiumei; Chen, Di; Chen, Huan; Wang, Wen; Liu, Yü; Wang, Yawei; Duan, Chao; Zhang, Ning; Guo, Xin; Otkur, Wuxiyar; Liu, Jing; Qi, Huan; Liu, Xiaolong; Liu, Hong‐Xu; Piao, Hulin

doi:10.1002/cac2.12164

Cited by 24 publications

(19 citation statements)

References 64 publications

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“…YBX1 was also found to be upregulated in HCC and was negatively associated with the overall survival in our analysis. Other studies confirmed the proposed oncogenic effect of YBX1 in HCC [ 48 , 77 , 78 ]. YBX1 has a wide variety of functions and acts also as RBP and influences RNA stability, splicing and translation [ 65 ].…”

Section: Discussionsupporting

confidence: 61%

Circular RNA hsa_circ_0062682 Binds to YBX1 and Promotes Oncogenesis in Hepatocellular Carcinoma

Razpotnik

Vidmar

Fonović

et al. 2022

Cancers

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Circular RNAs (circRNAs) have been shown to play an important role in the pathogenesis of hepatocellular carcinoma (HCC). By implementing available transcriptomic analyses of HCC patients, we identified an upregulated circRNA hsa_circ_0062682. Stable perturbations of hsa_circ_0062682 in Huh-7 and SNU-449 cell lines influenced colony formation, migration, cell proliferation, sorafenib sensitivity, and additionally induced morphological changes in cell lines, indicating an important role of hsa_circ_0062682 in oncogenesis. Pathway enrichment analysis and gene set enrichment analysis of the transcriptome data from hsa_circ_0062682 knockdown explained the observed phenotypes and exposed transcription factors E2F1, Sp1, HIF-1α, and NFκB1 as potential downstream targets. Biotinylated oligonucleotide pulldown combined with proteomic analyses identified protein interaction partners of which YBX1, a known oncogene, was confirmed by RNA immunoprecipitation. Furthermore, we discovered a complex cell-type-specific phenotype in response to the oncogenic potential of hsa_circ_0062682. This finding is in line with different classes of HCC tumours, and more studies are needed to shed a light on the molecular complexity of liver cancer.

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Section: Discussionsupporting

confidence: 61%

Circular RNA hsa_circ_0062682 Binds to YBX1 and Promotes Oncogenesis in Hepatocellular Carcinoma

Razpotnik

Vidmar

Fonović

et al. 2022

Cancers

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“…An increasing number of studies have demonstrated that non-m 6 A RNA modification regulators are significantly correlated with MES transition. It has been reported that ADAR and YBX1 promote MES transition by regulating oncogenic microRNA maturation ( 65 , 66 ). Nevertheless, research on RNA modifications beyond m 6 A is still not as mature as that for m 6 A for many reasons, including technology limitations.…”

Section: Introductionmentioning

confidence: 99%

The Non-N6-Methyladenosine Epitranscriptome Patterns and Characteristics of Tumor Microenvironment Infiltration and Mesenchymal Transition in Glioblastoma

Gao

Liu

et al. 2022

Front. Immunol.

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BackgroundAn increasing number of RNA modification types other than N6-methyladenosine (m6A) modification have been detected. Nonetheless, the probable functions of RNA modifications beyond m6A in the tumor microenvironment (TME), mesenchymal (MES) transition, immunotherapy, and drug sensitivity remain unclear.MethodsWe analyzed the characteristics of 32 non-m6A RNA modification regulators in 539 glioblastoma (GBM) patients and the TME cell infiltration and MES transition patterns. Using principal component analysis, a non-m6A epitranscriptome regulator score (RM score) model was established. We estimated the association between RM score and clinical characteristics, TME status, GBM subtypes, and drug and immunotherapy response.ResultsThree definite non-m6A RNA modification patterns associated with diverse biological pathways and clinical characteristics were identified. The high RM score group was characterized by a poor prognosis, enhanced immune infiltration, and MES subtype. Further analysis indicated that the high RM score group had a lower tumor mutation burden as well as a weaker response to immunotherapy. The higher RM score group may benefit more from drugs targeting the EGFR and WNT signaling pathways.ConclusionOur study exposed the potential relationship of non-m6A RNA modification regulators with clinical features, TME status, and GBM subtype and clarified its therapeutic value.

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“…This protein is also found in mRNP complexes and may play a role in microRNA processing. The possibility of YBX1-binding to multiple motifs distributed across the mRNA coding Spike could reduce cytoplasmic protein availability [ 25 , 26 ].…”

Section: Resultsmentioning

confidence: 99%

An in silico pipeline approach uncovers a potentially intricate network involving spike SARS-CoV-2 RNA, RNA vaccines, host RNA-binding proteins (RBPs), and host miRNAs at the cellular level

Chetta

Tarsitano

Oro

et al. 2022

Journal of Genetic Engineering and Biotechnology

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Background In the last 2 years, we have been fighting against SARS-CoV-2 viral infection, which continues to claim victims all over the world. The entire scientific community has been mobilized in an attempt to stop and eradicate the infection. A well-known feature of RNA viruses is their high mutational rate, particularly in specific gene regions. The SARS-CoV-2 S protein is also affected by these changes, allowing viruses to adapt and spread more easily. The vaccines developed using mRNA coding protein S undoubtedly contributed to the “fight” against the COVID-19 pandemic even though the presence of new variants in the spike protein could result in protein conformational changes, which could affect vaccine immunogenicity and thus vaccine effectiveness. Results The study presents the findings of an in silico analysis using various bioinformatics tools finding conserved sequences inside SARS-CoV-2 S protein (encoding mRNA) same as in the vaccine RNA sequences that could be targeted by specific host RNA-binding proteins (RBPs). According to the results an interesting scenario emerges involving host RBPs competition and subtraction. The presence of viral RNA in cytoplasm could be a new tool in the virus’s armory, allowing it to improve its chances of survival by altering cell gene expression and thus interfering with host cell processes. In silico analysis was used also to evaluate the presence of similar human miRNA sequences within RBPs motifs that can modulate human RNA expression. Increased cytoplasmic availability of exogenous RNA fragments derived from RNA physiological degradation could potentially mimic the effect of host human miRNAs within the cell, causing modulation of the host cell network. Conclusions Our in silico analysis could aid in shedding light on the potential effects of exogenous RNA (i.e. viruses and vaccines), thereby improving our understanding of the cellular interactions between virus and host biomolecules. Finally, using the computational approach, it is possible to obtain a safety assessment of RNA-based vaccines as well as indications for use in specific clinical conditions.

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YB1 regulates miR‐205/200b‐ZEB1 axis by inhibiting microRNA maturation in hepatocellular carcinoma

Cited by 24 publications

References 64 publications

Circular RNA hsa_circ_0062682 Binds to YBX1 and Promotes Oncogenesis in Hepatocellular Carcinoma

Circular RNA hsa_circ_0062682 Binds to YBX1 and Promotes Oncogenesis in Hepatocellular Carcinoma

The Non-N6-Methyladenosine Epitranscriptome Patterns and Characteristics of Tumor Microenvironment Infiltration and Mesenchymal Transition in Glioblastoma

An in silico pipeline approach uncovers a potentially intricate network involving spike SARS-CoV-2 RNA, RNA vaccines, host RNA-binding proteins (RBPs), and host miRNAs at the cellular level

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