Transcriptomic analyses of gene expression by CRISPR knockout of miR-214 in cervical cancer cells

Sen, Prakriti; Ghosal, Sayam; Hazra, Rudranil; Arega, Solomon; Mohanty, Rimjhim; Kulkarni, Kirti; Budhwar, Roli; Ganguly, Niladri

doi:10.1016/j.ygeno.2019.08.020

Cited by 17 publications

(9 citation statements)

References 32 publications

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“…SP3 binds GT-and GC-box promoter elements and competes with SP1 for binding the GC-box promoter-a mechanism that regulates gene transcription [35]. SP3 is dysregulated in various cancers and is highly expressed in HCC [36][37][38][39]. Sp3 decreases the sensitivity of Hep3B cells to chemotherapy, and it uses MALAT1 to regulate HCC [39,40].…”

Section: Discussionmentioning

confidence: 99%

Hsa_circ_0011385 knockdown represses cell proliferation in hepatocellular carcinoma

Yang

et al. 2021

Cell Death Discov.

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Circular RNAs (circRNAs), continuous loops of single-stranded RNA, regulate gene expression during the development of various cancers. However, the function of circRNAs in hepatocellular carcinoma (HCC) is rarely discussed. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to determine the mRNA levels of circ_0011385, miR-361-3p, and STC2 in 96 pairs of HCC tissues (tumor tissues and adjacent normal tissues), HCC cell lines, and L02 (human normal liver cell line) cells. The relationships between circ_0011385 expression and clinical features of HCC were evaluated. Functional experiments in vitro or in vivo were used to evaluate the biological function of circ_0011385. Bioinformatics analysis was performed to predict miRNAs and mRNAs sponged by circ_0011385. RNA immunoprecipitation (RIP) and dual-luciferase reporter gene assays were used to elucidate the interactions among circ_0011385, miR-361-3p, and STC2 (stanniocalcin 2). ChIP and dual-luciferase reporter gene assays were used to identify the upstream regulator of circ_0011385. High expression of circ_0011385 was observed in HCC tissues and cell lines and was significantly associated with tumor size, TNM stage, and prognosis. In addition, inhibition of circ_0011385 expression prevented the proliferation of HCC cells in vitro and in vivo. Circ_0011385 sponged miR-361-3p, thereby regulating the mRNA expression of STC2. In addition, the transcription of circ_0011385 was regulated by SP3. Circ_0011385 knockdown suppressed cell proliferation and tumor activity in HCC. Circ_0011385 may therefore serve as a new biomarker in the diagnosis and treatment of HCC.

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Section: Discussionmentioning

confidence: 99%

Hsa_circ_0011385 knockdown represses cell proliferation in hepatocellular carcinoma

Yang

et al. 2021

Cell Death Discov.

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“…Dysregulation or dysfunction of miRNAs may participate in the progression of cancer, manifesting the intimate correlations with the development, progression and prognosis of cervical cancer. At present, enormous studies are investigating the relationship between cervical cancer and miRNAs, including miR-137, miR-574-5p and miR-21, and involvement of these miRNAs in the development and progression of cervical cancer (3,21,27). But there remains no evidence suggesting the molecular mechanism of miRNA in the development and progression of cervical cancer.…”

Section: Discussionmentioning

confidence: 99%

MiRNA-214 promotes the pyroptosis and inhibits the proliferation of cervical cancer cells via regulating the expression of NLRP3

Zhao

et al. 2020

Cell Mol Biol (Noisy-le-grand)

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Inflammasome mediates the maturation of interleukin-1Î² (IL-1Î²) and IL-18, triggers the pyroptosis and associates with multiple autoimmune diseases. In light of this, we hope to investigate the regulatory role of miRNA-214 in the inflammasome of cervical cancer. With the samples collected from 50 cervical cancer patients and 50 age-matched healthy subjects, real-time PCR and Western blotting were employed to detect the mRNA and/or protein expression profiles of the NOD-like receptor protein family, including NLRP1, NLRP3, NLRC4, Caspase-1, IL-1Î², IL-18 and miR-214. Corresponding plasmids were used to transfect the Hela, HCC94, Siha or HUCEL normal cell lines to upregulate or downregulate the expression of targeted genes and to construct the cervical cancer models on rats. In addition, RT-PCR and Western blot were also considered to detect the expression of miR-214 and pyroptosis-related genes, while the pyroptosis of cells was evaluated by using the caspase-1 activity detection kit. Downregulation of miR-214 was found in the cervical cancer patients and the cervical cancer cell lines (** P <0.01), while overexpression of miR-214 could induce the pyroptosis of cervical cancer cell by targeting NLRP3. In cervical cancer patients, miR-214 and NLRP3 are downregulated, while upregulation of miR-214, by enhancing the expression of NLRP3, can advance the pyroptosis of cervical cancer cells. In addition, we, for the first time, clarify the correlation of cervical cancer with the miR-214 and NLRP3.

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“…The expression levels of these different types of RNA transcripts from Notch2-shRNA treated samples were compared with control samples. The differentially expressed transcripts from treated samples were identified using Cuff Diff pipeline with a fold change cutoff of ≥ 1.5 and a student t-test P-value of ≤ 0.05 upon treatment [29,30]. From this analysis, we have identified 1,067 statistically significant transcripts.…”

Section: Distribution Of Dets Based On Transcript Typementioning

confidence: 99%

RNA sequencing analyses reveal differentially expressed genes and pathways as Notch2 targets in B-cell lymphoma

2020

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Splenic marginal zone lymphoma (SMZL) is a low grade, indolent B-cell neoplasm that comprises approximately 10% of all lymphoma. Notch2, a pivotal gene for marginal zone differentiation is found to be mutated in SMZL. Deregulated Notch2 signaling has been involved in tumorigenesis and also in B-cell malignancies. However the role of Notch2 and the downstream pathways that it influences for development of B-cell lymphoma remains unclear. In recent years, RNA sequencing (RNA-Seq) has become a functional and convincing technology for profiling gene expression and to discover new genes and transcripts that are involved in disease development in a single experiment. In the present study, using transcriptome sequencing approach, we have identified key genes and pathways that are probably the underlying cause in the development of B-cell lymphoma. We have identified a total of 15,083 differentially expressed genes (DEGs) and 1067 differentially expressed transcripts (DETs) between control and Notch2 knockdown B cells. Gene Ontology (GO) term enrichment and pathway analysis were applied for the identification of key genes and pathways involved in development of B-cell lymphoma. In addition, intermediate genes of top canonical pathways such as PI3K/AKT and NF-kB were found to be downregulated with Notch2 knockdown, indicating that these pathways could be the putative downstream effectors through which Notch2 mediates its oncogenic effects. Taken collectively, the identified crop of genes and pathways may be considered as targets for the treatment of B-cell lymphoma.

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Transcriptomic analyses of gene expression by CRISPR knockout of miR-214 in cervical cancer cells

Cited by 17 publications

References 32 publications

Hsa_circ_0011385 knockdown represses cell proliferation in hepatocellular carcinoma

Hsa_circ_0011385 knockdown represses cell proliferation in hepatocellular carcinoma

MiRNA-214 promotes the pyroptosis and inhibits the proliferation of cervical cancer cells via regulating the expression of NLRP3

RNA sequencing analyses reveal differentially expressed genes and pathways as Notch2 targets in B-cell lymphoma

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