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ILF2 Regulates RNA Splicing of DNA Damage Response Genes to Confer Poor Prognosis in 1q21-Amplified Multiple Myeloma

ABSTRACT: To understand whether ILF2 is required to ensure the alternative splicing and processing of specific pre-mRNAs in Multiple Myeloma (MM), both in physiological and DNA damage conditions, we performed RNA sequencing (RNA-Seq) analysis of untreated or melphalan-treated ILF2-depleted JJN3 cells. Non-silencing or ILF2 shRNA transduced JJN3 cells were treated with melphalan for 10 hours.

ORGANISM(S): Homo sapiens

PROVIDER: GSE83712 | GEO | 2017/01/01

SECONDARY ACCESSION(S): PRJNA326776

REPOSITORIES: GEO

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RNA immunoprecipitation and sequencing of ILF2-bound transcripts in Multiple Myeloma

Project description:To understand the mechanistic basis of ILF2’s regulation of mRNA splicing in response to DNA damage in Multiple Myeloma, we performed RNA immunoprecipitation (RIP) and sequencing of ILF2-bound transcripts under both physiological and DNA damage (melphalan treatment) conditions. Cells were treated with melphalan for 10 hours. RNA immunopreciptation (RIP) and sequencing of ILF2-bound RNAs was performed in the JJN3 and H929 cell lines (two biological replicates/condition). Cells were treated with melphalan for 10 hours.

2017-05-23 | GSE83662 | GEO

RNA immunoprecipitation and sequencing of YB-1-bound transcripts in Multiple Myeloma

Project description:To understand the mechanistic basis of YB-1’s regulation of mRNA splicing in response to DNA damage in Multiple Myeloma, we performed RNA immunoprecipitation (RIP) and sequencing of ILF2-bound transcripts under both physiological and DNA damage (melphalan treatment) conditions. Cells were treated with melphalan for 10 hours. (RIP) and sequencing of YB-1-bound RNAs was performed in the JJN3 line (two biological replicates/condition).

2017-05-23 | GSE83664 | GEO

ILF2 Regulates RNA splicing of DNA Damage Response Genes to confer poor prognosis in 1q21-Amplified Multiple Myeloma

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-05-23 | GSE83665 | GEO

Treatment of MM cells with non-targeting (NT) or ILF2 targeting oligonucleotide antisenses (ASOs)

Project description:To gain insights into the molecular mechanisms by which myeloma cells overcome ILF2 ASO-induced DNA damage activation, we performed bulk RNA sequencing (RNA-seq) analysis of ASO-treated KMS11 and JJN3 cells at early (1 week) and late (3 weeks) treatment time points.

2023-11-28 | GSE192944 | GEO

ILF2 Regulates RNA splicing of DNA Damage Response Genes to confer poor prognosis in 1q21-Amplified Multiple Myeloma

Project description:ILF2 Regulates RNA splicing of DNA Damage Response Genes to confer poor prognosis in 1q21-Amplified Multiple Myeloma

| PRJNA326671 | ENA

Homo sapiens

Project description:RNA-sequencing analysis of untreated or melphalan treated non silencing or ILF2 shRNA-transduced JJN3 cells

| PRJNA326690 | ENA

Exploring ILF2 regulatory genes by next-generation sequencing

Project description:We knocked down the expression of ILF2 in the A549 cell line and sequenced the RNA genes with the untreated A549 cells to find the regulatory gene of ILF2.

2019-06-06 | GSE126475 | GEO

Knockdown of ILF2/ILF3 (NF45/NF90) in the gastric cancer cell line SGC7901

Project description:Our data showed that lncRNA ELF3-AS1 could bind on the exon1 of ELF3-201 to form a double-stranded RNA molecule. This double-stranded RNA could interact with ILF2/ILF3 complex. To explore the biofunction of the interaction between ELF3-AS1 and ILF2/ILF3 complex, loss-of-function studies regarding ILF2 and ILF3 were performed in SGC7901 cell line. RNA sequencing studies showed that knockdown of ILF3 significantly decreased ELF3-AS1, while knockdown of ILF2 significantly increased ELF3-AS1 and NF90 expression. Our data revealed that ILF2/ILF3 complex interacted with ELF3-AS1/ELF3 double-stranded RNA and regulated their transcripts stability.

2021-10-01 | GSE161544 | GEO

Identification the proteins interacted with ILF2 in human keratinocytes

Project description:By profiling lncRNA expression changes during human skin wound healing and screening lncRNA functions, we identified SNHG26 as a pivotal regulator in keratinocyte progenitors underpinning this phase transition. we performed RNA pull-down assay in human keratinocyte progenitors and found SNHG26 interact with ILF2. ILF2, or the nuclear condensates it forms, is crucial for maintaining the stability of SNHG26. To identify other protein components within these condensates, we employed a proximity-dependent biotin identification (BioID) assay, which label proteins in close proximity to ILF2 that fused to BioID2, and subsequently identifying them through mass spectrometry (MS).

2024-08-28 | PXD055235 | Pride

ILF2 Is a Regulator of RNA Splicing and DNA Damage Response in 1q21-Amplified Multiple Myeloma.

Project description:Amplification of 1q21 occurs in approximately 30% of de novo and 70% of relapsed multiple myeloma (MM) and is correlated with disease progression and drug resistance. Here, we provide evidence that the 1q21 amplification-driven overexpression of ILF2 in MM promotes tolerance of genomic instability and drives resistance to DNA-damaging agents. Mechanistically, elevated ILF2 expression exerts resistance to genotoxic agents by modulating YB-1 nuclear localization and interaction with the splicing factor U2AF65, which promotes mRNA processing and the stabilization of transcripts involved in homologous recombination in response to DNA damage. The intimate link between 1q21-amplified ILF2 and the regulation of RNA splicing of DNA repair genes may be exploited to optimize the use of DNA-damaging agents in patients with high-risk MM.

| S-EPMC5593798 | biostudies-literature

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