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Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events

ABSTRACT: To identify genes regulated by NFE2L2 (Nrf2), we selected a lung cancer cell line (A549) in which NFE2L2 is normally active. Three transfections using siRNAs targeting NFE2L2 and four control transfections using two different negative control siRNAs were done. As a result, we found several genes up or down regulated in response to NFE2L2 inactivation in these cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE75452 | GEO | 2016/10/25

REPOSITORIES: GEO

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Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events

Project description:To identify genes regulated by NFE2L2 (Nrf2), we selected a lung cancer cell line (A549) in which NFE2L2 is normally active. Three transfections using siRNAs targeting NFE2L2 and four control transfections using two different negative control siRNAs were done. As a result, we found several genes up or down regulated in response to NFE2L2 inactivation in these cells. A549 cells were cultured, and 250,000 cells were transfected with Lipofectamine RNAiMAX reagent containing 5 nmol siRNA particles in a 6-well plate. Three transfections with siRNAs targeting NFE2L2 were performed, using three independent duplexes, while four control transfections were done using two different control duplexes, in addition to one mock (Lipofectamine only) transfection. RNA was prepared using the RNeasy Mini kit. 8 strand-specific total RNA-seq libraries were generated on an Illumina NextSeq 500. Between 50.5 and 60.6 million reads were obtained per sample. Reads were aligned to hg19 genome, at an alignment rate exceeding 94.4% for all samples.

2016-10-25 | E-GEOD-75452 | biostudies-arrayexpress

Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events.

Project description: Not available

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ChIP-Seq analysis of NRF2 binding sites in human BEAS-2B cell line treated with sulforaphane or vehicle

2018-06-19 | GSE75812 | GEO

Identification of Novel NRF2-Regulated Genes by ChIPSeq

Project description:Cellular oxidative and electrophilic stress triggers a protective response in mammals regulated by NRF2 (nuclear factor (erythroid-derived) 2-like; NFE2L2) binding to DNA-regulatory sequences near stress responsive genes. Studies using Nrf2-deficient mice suggest that hundreds of genes may be regulated by NRF2. To identify human NRF2-regulated genes, we conducted ChIP-sequencing experiments in lymphoid cells treated with the dietary isothiocyanate, sulforaphane (SFN) and carried out follow-up biological experiments on candidates. We found 242 high-confidence, NRF2-bound genomic regions and 96% of these regions contained NRF2-regulatory sequence motifs. The majority of binding sites were near potential novel members of the NRF2 pathway. Validation of selected candidate genes using parallel ChIP techniques and in NRF2-silenced cell lines indicated that the expression of about two thirds of the candidates are likely to be directly NRF2-dependent including retinoid X receptor alpha (RXRA). NRF2 regulation of RXRAhas implications for response to retinoid treatments and adipogenesis. In mouse 3T3-L1 cells SFN treatment affected Rxra expression early in adipogenesis and knockdown of Nrf2 delayed Rxra expression, both leading to impaired adipogenesis. ChIP-Seq analysis of NRF2 binding sites in human lymphoblastoid cells treated with sulforaphane or vehicle

2012-06-18 | E-GEOD-37589 | biostudies-arrayexpress

Comparison of the transcriptomic impact of NRF2 depletion with that of NUAK1 depletion in SW480 colorectal cancer cells

Project description:The intent of the experiment is to determine how much of NRF2 (NFE2L2)-dependent transcription requires NUAK1 upstream. SW480 cells were transfected with siRNA targeting either NRF2, NUAK1 or non-targeting control, and harvested for analysis by RNA-SEQ 48hrs after transfection. mRNA was analysed by Illumina paired-end RNA-SEQ

2018-02-19 | E-MTAB-6264 | biostudies-arrayexpress

Analysis of NFE2L2 (NRF2) binding to chromatin in primary human keratinocytes

Project description:Analysis of NFE2L2 (NRF2) binding to chromatin in primary human keratinocytes

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Discovering novel driver mutations from pan-cancer analysis of mutational and gene expression profiles.

Project description: Not available

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Identification of Novel NRF2-Regulated Genes by ChIPSeq

2012-06-18 | GSE37589 | GEO

Identification of Novel NRF2-Regulated Genes by ChIPSeq

2012-06-18 | GSE37589 | GEO

A Conditional Mouse Expressing a Tumor-derived Mutation in the NRF2 Transcription Factor Displays Hyperplasia of the Upper Gastrointestinal Tract and Decreased White Adipose Fat

Project description:Activation of the nuclear factor (erythroid-derived 2)-like 2 (NFE2L2 or NRF2) transcription factor is a critical and evolutionarily conserved cellular response to oxidative stress, metabolic stress, and xenobiotic insult. Whereas NRF2 deficiency results in hypersensitivity to a variety of stressors, its aberrant activation contributes to several cancer types, most commonly squamous cell carcinomas of the oesophagus, oral cavity, bladder and lung. Between 10-35% of patients with squamous cell carcinomas display hyperactive NRF2 signaling, harboring activating mutations and copy number amplifications of the NFE2L2 oncogene or inactivating mutations or deletions of KEAP1 or CUL3, which co-complex to ubiquitylate and degrade NRF2 protein. To better understand the role of NRF2 in tumorigenesis and more broadly in development, we engineered the endogenous Nfe2l2 genomic locus to create a conditional mutant LSL-Nrf2E79Q mouse model. The NRF2E79Q mutant protein does not undergo KEAP1/CUL3-dependent degradation, resulting in its constitutive activity. The E79Q mutation is also one of the most commonly observed NRF2-activating mutations in human squamous cancers. Expression of NRF2E79Q protein in keratin 14 (Krt14)-positive murine tissues resulted in a stunted body axis, decreased weight, decreased adipocyte size, and hyperplasia of squamous cell tissues of the tongue, forestomach, and oesophagus. RNAseq profiling and follow-up validation studies of cultured Nrf2E79Q murine esophageal epithelial cells revealed known and novel NRF2-regulated transcriptional programs, including genes associated with squamous cell carcinoma (e.g. Myc), lipid and cellular metabolism (Hk2, Ppard), and growth factors (Areg, Bmp6, Vegfa). These data suggest that in addition to decreasing adipogenesis, KRT14 restricted NRF2 activation leads to hyperplasia of the oesophagus, forestomach and tongue, but notably is not sufficient to drive formation of squamous cell carcinoma.

2020-06-23 | GSE141311 | GEO

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