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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and hnRNPA2B1-KO sw480 cell line Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and hnRNPA2B1-KO sw480 cell line Transcriptomes

PROVIDER: PRJNA715714 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and hnRNPA2B1-KO sw480 cell line Transcriptomes

Project description:HNRNPA2B1, an RNA-binding protein, plays a key role in primary microRNA processing, alternative splicing, mRNA metabolism and transport. Interestingly, hnRNPA2B1 also works as an N6-methyladenosine(m6A) reader and is critical during tumorigenesis of various tissue types. However, its role in colon cancer is still unclear. In this study, we aimed to elucidate the biological functions of hnRNPA2B1 and to explore its underlying mechanisms in colon cancer. Methods We examined the expression of hnRNPA2B1 in Oncomine and TCGA databases. Then verified the findings in colon cancer cells and clinical samples with western blotting and immunohistochemistry (IHC). We used CRISPR/Cas9 directed gene editing to knockout hnRNPA2B1 expression in human colon cancer cell line SW480 and carried out both in vivo and in vitro experiments. The results were further confirmed by RNA-seq analysis. We found that hnRNPA2B1 significantly promoted colon cancer cell proliferation both in vitro and in vivo, while knockout of hnRNPA2B1 induced apoptosis and cell cycle arrest in SW480. RNA-seq analysis revealed that the ERK/MAPK pathway was activated by hnRNPA2B1 upregulation. In addition, both hnRNPA2B1 and MAPK pathway were activated in clinical colon cancer specimens and positively correlated. Mechanistically, hnRNPA2B1 appeared to be an upstream regulator of the ERK/MAPK pathway and inhibition of MAPK signaling blocked the effects of hnRNPA2B1. Taken together, our data demonstrated that the RNA-binding protein hnRNPA2B1 promotes cell proliferation and regulates cell cycle and apoptosis of human colon cancer by activating the ERK/MAPK signaling, which may provide a new insight into the development of hnRNPA2B1 as a potential therapeutic target for treatment of colon cancer.

2021-06-09 | GSE169211 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

Project description:Heparanase (HPSE), the only known mammalian endoglycosidase responsible for heparan sulfate cleavage, is a multi-faceted protein affecting multiple malignant behaviors in cancer cells. The goals of this study are to compare the mRNA transcriptome differences between SW480 cells and HPSE-knockdown SW480 cells. Methods: mRNA profiles of SW480 cells and HPSE-knockdown SW480 cells were generated by deep sequencing, in triplicate, using Illumina.

2019-02-14 | GSE126504 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

| PRJNA522246 | ENA

Nuclear HNRNPA2B1 HITS-CLIP and RNA-seq

Project description:To identify HNRNPA2B1 binding sites on endogenous nuclear RNAs, we performed HITS-CLIP for endogenous HNRNPA2B1 and RNA-seq to analyze the nuclear RNA under either METTL3 or HNRNPA2B1 depletion. Wild type MDA-MB-231 cells were subjected to the HITS-CLIP procedure on immunoprecipitated HNRNPA2B1 associated RNA obtained from the nuclear fraction (Licatalosi D, et al. 2008, Nature 456:464-U22). For RNA-seq, nuclear RNA was extracted from MDA-MB-231 or Hela cells knocked down for METTL3 or HNRNPA2B1.

2015-06-20 | E-GEOD-70061 | biostudies-arrayexpress

Nuclear HNRNPA2B1 HITS-CLIP and RNA-seq

2015-06-20 | GSE70061 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of colorectal cancer cell lines including SW480 and SW620

Project description:Purpose: The goals of this study are to compare the differentially expressed miRNAs between SW480 and SW620. Methods:Total RNA of two samples was used to prepare the miRNA sequencing library.The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq. Results:We found 72 miRNAs were downregulated on the basis of fold-change less than 0.5. However,total 160 miRNAs were upregulated on the basis of fold-change greater than 2. Conclusions: Our study represents the detailed analysis of SW480 and SW620, generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of miRNA content. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-01-22 | GSE144002 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of IFNα Stimulated Transcriptomes in HepG2, SETD2-KO, STAT1-KO and STAT1-K525ARe HepG2 cells

Project description:Purpose: Using RNA-seq to analyze the different expressions induced by IFNα among the SETD2-KO HepG2 cells, STAT1-KO HepG2 cells and STAT1-K525A-Re HepG2 cells and HepG2 control cells Methods: mRNA profiles of HepG2 control cells and SETD2-KO cells, STAT1-KO cells, STAT1-K525A-Re cells were generated by deep sequencing, using BGISEQ-500RS. The sequence reads that passed quality filters were analyzed at the transcriptional level with RSEM (RNA-seq by Expectation Maximization).

2019-03-12 | GSE98372 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of colorectal cancer cell lines including SW480 and SW620

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of colorectal cancer cell lines including SW480 and SW620

| PRJNA602485 | ENA

Transcriptome sequencing of the hnRNPA2B1 knockout Huh7 cell line

Project description:To investigate the role of hnRNPA2B1 in the progression of hepatocellular carcinogenesis, we established a Huh7 cell line in which the hnRNPA2B1 gene was knocked out by crisper/cas9.

2023-09-01 | GSE226544 | GEO

Sumoylated hnrnpa2b1 controls the sorting of miRNAs into two exosomes through binding to specific motifs

Project description:Exosomes are released by most cells to the extracellular environment, and are involved in cell-to-cell-communication. Exosomes contain specific repertoires of mRNAs, miRNAs and other non-coding RNAs that can be functionally transferred to recipient cells. However, the mechanisms that control the specific loading of RNA species into exosomes remain unknown. Here we describe short sequence motifs present in miRNAs that control their localization into exosomes. The protein hnRNPA2B1 specifically binds exosomal miRNAs through the recognition of these motifs and controls their loading into exosomes. Moreover, hnRNPA2B1 in exosomes is sumoylated, and sumoylation controls the binding of hnRNPA2B1 to miRNAs. The loading of miRNAs into exosomes can be modulated by mutagenesis of the identified motifs or changes in hnRNPA2B1 expression levels. These findings identify hnRNPA2B1 as a key player in miRNA sorting into exosomes and provide potential tools for the packaging of selected regulatory RNAs into exosomes and their use in biomedical applications.

2014-04-16 | PXD000350 | Pride

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