Next-generation sequencing reveals hsa_circ_0058092 being a potential oncogene candidate involved in gastric cancer

Bu, Xuefeng; Zhang, Xuanfeng; Luan, Wenkang; Zhang, Riting; Zhang, Yao; Zhang, Anwei; Yan, Ye

doi:10.1016/j.gene.2019.144176

Cited by 7 publications

(13 citation statements)

References 25 publications

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“…Furthermore, IGF2BP3-circRNA interactions have been found in other types of cancer such as hsa_circ_0003258-IGF2BP3, CDR1as-IGF2BP3 and hsa_circ_0000231-IGF2BP3 35,47,48 . Given that abundant noncoding RNAs exist in eukaryotes 49,50 , a comprehensive identi cation of RNAs interacting with IGF2BP3 is helpful to understand the oncogenic role of IGF2BP3 in GC. In the present study, RIP combined with RNA sequencing uncovered a series of RNAs, including mRNAs and circRNAs, that interacted with IGF2BP3 in GC.…”

Section: Discussionmentioning

confidence: 99%

CircARID1A binds to IGF2BP3 in gastric cancer and promotes cancer proliferation by forming a circARID1A-IGF2BP3-SLC7A5 RNA-protein ternary complex

Yang

Huang

et al. 2022

Preprint

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Background Gastric cancer (GC) is one of the most common malignant tumors in China. Circular RNAs (circRNAs) are novel non-coding RNAs with important regulatory roles in cancer progression. IGF2BP3 has been found to play oncogenic roles in various cancers including GC, while the exact mechanism of IGF2BP3 is largely unknown. Methods The expression of IGF2BP3 in GC was evaluated by Western Blot and bioinformatics analysis. CircRNA expression profiles were screened via IGF2BP3 RIP-seq in GC. Sanger sequencing, RNase R digestion, nucleo-plasmic separation and RNA-FISH assays were used to detect the existence and expression of circARID1A. RNA ISH assay was employed to test the expression of circARID1A in paraffin-embedded GC tissues. Moreover, the function of circARID1A on cellular proliferation was assessed by CCK-8, plate colony formation, EdU assays and GC xenograft mouse model in vivo. Furthermore, the location or binding of circARID1A, IGF2BP3 protein and SLC7A5 in GC was evaluated by RNA-FISH/IF or RNA pull-down assays. Results We identified a novel circRNA, circARID1A, that can bind to IGF2BP3 protein. CircARID1A was significantly upregulated in GC tissues compared with noncancerous tissues and positively correlated with tumor length, tumor volume, and TNM stage. CircARID1A knockdown inhibited the proliferation of GC cells in vitro and in vivo and circARID1A was indispensable for the oncogenic role of IGF2BP3. Mechanistically, circARID1A served as a scaffold to facilitate the interaction between IGF2BP3 and SLC7A5 mRNA, increasing SLC7A5 mRNA stability. Additionally, circARID1A was able to directly bind SLC7A5 mRNA through complementary base-pairing and then formed the circARID1A-IGF2BP3-SLC7A5 RNA-protein ternary complex and promoted the proliferation of GC via AKT/mTOR pathway activation. Conclusions Altogether, our data suggest that circARID1A is involved in the function of IGF2BP3 and GC proliferation, and the circARID1A-IGF2BP3-SLC7A5 axis has the potential to serve as a new therapeutic target for GC.

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Section: Discussionmentioning

confidence: 99%

CircARID1A binds to IGF2BP3 in gastric cancer and promotes cancer proliferation by forming a circARID1A-IGF2BP3-SLC7A5 RNA-protein ternary complex

Yang

Huang

et al. 2022

Preprint

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“…The expression of hsa_circ_0032254 and hsa_circ_0032875 was correlated with FYN, SELENBP1 and GRIPAP1. The hsa_circ_0032254 has been shown to be related to gastric cancer [25]. However, there is no reported in epilepsy.…”

Section: Discussionmentioning

confidence: 99%

Profiling Analysis of Circular RNA and mRNA in Human Temporal Lobe Epilepsy with Hippocampal Sclerosis ILAE Type 1

Wang

et al. 2021

Cell Mol Neurobiol

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Hippocampal sclerosis (HS) is the most common surgical pathology associated with temporal lobe epilepsy (TLE). However, the cause of TLE with or without HS remains unknown. Our current study aimed to illustrate the essential molecular mechanism that are potentially involved in the pathogenesis of TLE-HS and to shed light on the transcriptional changes associated with hippocampal sclerosis. RNA-seq analysis was performed to evaluate profiling of circRNAs and mRNAs in hippocampal tissues of HS IALE-type 1 and no-HS patients. Systematic bioinformatic analysis of expression levels was utilized in circRNAs and mRNAs. Altered expression of selected circRNAs and mRNAs levels was confirmed by RT-PCR. In this study, we explored transcriptomic profiling of circRNAs and mRNAs expression in 3 ILAE type 1 and 3 no-HS hippocampal tissues.Compared to no-HS group, 341 mRNA transcripts and 133 circRNA transcripts were differentially expressed in ILAE type 1 group. Gene Ontology analysis demonstrated that the dysregulated genes were associated with the biological processes of vesicle-mediated transport. Enrichment analysis demonstrated that dysregulated genes were involved mainly in the mitogen-activated protein kinase (MAPK) signal pathway. Subsequently, A total of 441 known or predicted interactions were formed among DEGs, and the most important module was detected in the PPI network using the MCODE plug-in. There were mainly four functional modules enriched: ER to Golgi transport vesicle membrane, Basal transcription factors, GABA-gated chloride ion channel activity, CENP-A containing nucleosome assembly. A circRNA-mRNA co-expression network was constructed including 5 circRNAs(hsa_circ_0025349, hsa_circ_0002405, hsa_circ_0004805, hsa_circ_0032254, and hsa_circ_0032875) and three mRNAs (FYN, SELENBP1, and GRIPAP1)based on the normalized mRNA signal intensities. This is the first to report the circRNAs and mRNAs expression profile of surgically resected hippocampal tissues from TLE patients of ILAE-1 and no-HS, and these results may provide new insight on the transcriptional changes associated with this pathology.

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“…The expression of hsa_circ_0032254 and hsa_circ_0032875 was correlated with FYN, SELENBP1 and GRIPAP1. The hsa_circ_0032254 is related to gastric cancer (Bu et al 2020). However, there is no report in epilepsy.…”

Section: Discussionmentioning

confidence: 99%

Profiling Analysis of Circular RNA and mRNA in Human Temporal Lobe Epilepsy with Hippocampal Sclerosis ILAE Type 1

Wang

et al. 2021

Preprint

View full text Add to dashboard Cite

Hippocampal sclerosis (HS) is the most common surgical pathology associated with temporal lobe epilepsy (TLE). However, the cause of TLE with or without HS remains unknown. Our current study aimed to illustrate the essential molecular mechanism that is potentially involved in the pathogenesis of TLE-HS and to shed light on the transcriptional changes associated with hippocampal sclerosis. Compared to no-HS group, 341 mRNA transcripts and 131 circRNA transcripts were differentially expressed in ILAE type 1 group. The raw sequencing data have been deposited into sequence read archive (SRA) database under accession number PRJNA699348.Gene Ontology analysis demonstrated that the dysregulated genes were associated with the biological processes of vesicle-mediated transport. Enrichment analysis demonstrated that dysregulated genes were involved mainly in the MAPK signal pathway. Subsequently, A total of 441 known or predicted interactions were formed among DEGs, and the most important module was detected in the PPI network using the MCODE plug-in. There were mainly four functional modules enriched: ER to Golgi transport vesicle membrane, Basal transcription factors, GABA-gated chloride ion channel activity, CENP-A containing nucleosome assembly. A circRNA-mRNA co-expression network was constructed including 5 circRNAs(hsa_circ_0025349, hsa_circ_0002405, hsa_circ_0004805, hsa_circ_0032254, and hsa_circ_0032875) and three mRNAs (FYN, SELENBP1, and GRIPAP1) based on the normalized mRNA signal intensities. This is the first to report the circRNAs and mRNAs expression profile of surgically resected hippocampal tissues from TLE patients of ILAE-1 and no-HS, and these results may provide new insight into the transcriptional changes associated with this pathology.

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Next-generation sequencing reveals hsa_circ_0058092 being a potential oncogene candidate involved in gastric cancer

Cited by 7 publications

References 25 publications

CircARID1A binds to IGF2BP3 in gastric cancer and promotes cancer proliferation by forming a circARID1A-IGF2BP3-SLC7A5 RNA-protein ternary complex

CircARID1A binds to IGF2BP3 in gastric cancer and promotes cancer proliferation by forming a circARID1A-IGF2BP3-SLC7A5 RNA-protein ternary complex

Profiling Analysis of Circular RNA and mRNA in Human Temporal Lobe Epilepsy with Hippocampal Sclerosis ILAE Type 1

Profiling Analysis of Circular RNA and mRNA in Human Temporal Lobe Epilepsy with Hippocampal Sclerosis ILAE Type 1

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