Characterizing the tumor RBP-ncRNA circuits by integrating transcriptomics, interactomics and clinical data

Jiang, Leiming; Chen, Qiuyang; Bei, Mingrong; Shao, Mengting; Xu, Jianzhen

doi:10.1016/j.csbj.2021.09.019

Cited by 8 publications

(5 citation statements)

References 76 publications

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“…MAGI2-AS3 genes known to bind RBPs have been reported. Jiang et al 31 have suggested that MAGI2-AS3 had high connections with RBPs and miRNAs in the pan-cancer network and the new role of a member of the pan-cancer RBP-ncRNA circuits hsa-miR-224-5p-MAGI2-AS3-MBNL2 in the EMT program. Subsequently, the abnormal expression of RBPs was closely correlated with the occurrence and development of malignant tumors; the RBP EIF4A3 was overexpressed in a considerable number of cancers and coordinated cell cycle and cell apoptosis 32 , 33 .…”

Section: Discussionmentioning

confidence: 99%

Hypermethylation-Mediated lncRNA MAGI2-AS3 Downregulation Facilitates Malignant Progression of Laryngeal Squamous Cell Carcinoma via Interacting With SPT6

et al. 2023

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Long noncoding RNAs (lncRNAs) have an effect on the occurrence and progression of a considerable number of diseases, especially cancer. Existing research has suggested that MAGI2 antisense RNA 3 (MAGI2-AS3) takes on a critical significance in the development of hepatocellular carcinoma and lung cancer. However, the functions of MAGI2-AS3 in laryngeal squamous cell carcinoma (LSCC) remain unclear. In this study, MAGI2-AS3 expression level in LSCC tissue and cell lines was detected, and the effect of MAGI2-AS3 overexpressed on LSCC phenotypes and the possible influence mechanisms were examined. MAGI2-AS3 was downregulated in the tissues of LSCC patients versus non-tumor tissues, and it was correlated with advanced TNM (tumor, node, metastasis) stage and lymph node metastases, as indicated by the results of this study. MAGI2-AS3 inhibited the proliferation, migration, and invasion of LSCC cells in vitro and in vivo. Furthermore, the hypermethylation level of the MAGI2-AS3 promoter region was indicated by bisulfite genomic sequencing and methylation-specific polymerase chain reaction, such that MAGI2-AS3 expression was downregulated. Besides, MAGI2-AS3 promoter hypermethylation was regulated by DNA methyltransferase 1 (DNMT1), and MAGI2-AS3 expression was reversed by 5-Aza-2′-deoxycytidine (5-Aza). Moreover, the result of the RNA pull-down experiment suggested that 38 proteins were enriched in the MAGI2-AS3 group versus the control group in TU177 cells. To be specific, SPT6 (ie, a conserved protein) was enriched by fold change >10. SPT6 knockdown reduced the antitumor effect of MAGI2-AS3 in TU177 and AMC-HN-8 cells. Meanwhile, SPT6 overexpression inhibited the proliferation, metastasis, and invasion of TU177 and AMC-HN-8 cells. As revealed by the above findings, DNMT1-regulated MAGI2-AS3 promoter hypermethylation led to downregulated MAGI2-AS3 expression, such that the presence and progression of LSCC were inhibited in an SPT6 binding-dependent manner.

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Section: Discussionmentioning

confidence: 99%

Hypermethylation-Mediated lncRNA MAGI2-AS3 Downregulation Facilitates Malignant Progression of Laryngeal Squamous Cell Carcinoma via Interacting With SPT6

et al. 2023

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“…This highlights the importance of elucidating the pathogenesis of cancer, thus designing better therapeutic interventions through the novel lens of RBP-ncRNA circuits. 46 , 47 …”

Section: Discussionmentioning

confidence: 99%

CRIT: Identifying RNA-binding protein regulator in circRNA life cycle via non-negative matrix factorization

Shao

Hao

Jiang

et al. 2022

Molecular Therapy - Nucleic Acids

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“…Since SR proteins cross-regulate shared target genes, including the transcripts of each other, and form a dense coordinated network [ 76 ], a systems biology approach can be applied to globally identify the most dysregulated SR protein–RNA circuits under cancer conditions. This complementary approach enables the researcher to simultaneously characterize all alterations in SR proteins and to balance their multifunctionality without being trapped into negligible details [ 77 , 78 ].…”

Section: Functional Mechanisms Of Sr Proteins In Cancermentioning

confidence: 99%

SR proteins in cancer: function, regulation, and small inhibitor

Bei,

2024

Cell Mol Biol Lett

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Alternative splicing of pre-mRNAs is a fundamental step in RNA processing required for gene expression in most metazoans. Serine and arginine-rich proteins (SR proteins) comprise a family of multifunctional proteins that contain an RNA recognition motif (RRM) and the ultra-conserved arginine/serine-rich (RS) domain, and play an important role in precise alternative splicing. Increasing research supports SR proteins as also functioning in other RNA-processing-related mechanisms, such as polyadenylation, degradation, and translation. In addition, SR proteins interact with N6-methyladenosine (m6A) regulators to modulate the methylation of ncRNA and mRNA. Dysregulation of SR proteins causes the disruption of cell differentiation and contributes to cancer progression. Here, we review the distinct biological characteristics of SR proteins and their known functional mechanisms during carcinogenesis. We also summarize the current inhibitors that directly target SR proteins and could ultimately turn SR proteins into actionable therapeutic targets in cancer therapy.

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Characterizing the tumor RBP-ncRNA circuits by integrating transcriptomics, interactomics and clinical data

Abstract: Graphical abstract

Cited by 8 publications

References 76 publications

Hypermethylation-Mediated lncRNA MAGI2-AS3 Downregulation Facilitates Malignant Progression of Laryngeal Squamous Cell Carcinoma via Interacting With SPT6

Hypermethylation-Mediated lncRNA MAGI2-AS3 Downregulation Facilitates Malignant Progression of Laryngeal Squamous Cell Carcinoma via Interacting With SPT6

CRIT: Identifying RNA-binding protein regulator in circRNA life cycle via non-negative matrix factorization

SR proteins in cancer: function, regulation, and small inhibitor

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